From 37fcbe2a19cc66e839480528b5d1f43c5af7bb3d Mon Sep 17 00:00:00 2001
From: lecook <lecook@student.unimelb.edu.au>
Date: Tue, 7 Dec 2021 22:53:36 +1100
Subject: [PATCH] change folders

---
 .DS_Store                                     | Bin 8196 -> 6148 bytes
 whole-genome-alignment/.DS_Store              | Bin 0 -> 6148 bytes
 whole-genome-alignment/README.md              | 517 +++++++++++++
 whole-genome-alignment/env/wga.yaml           | 153 ++++
 whole-genome-alignment/scripts/alignment_QC.R |  90 +++
 .../scripts/array_wrapper.slurm               |  48 ++
 .../scripts/axtChain_commands.sh              | 718 +++++++++++++++++
 .../scripts/chainSort_commands.sh             | 713 +++++++++++++++++
 .../scripts/changeFilenameLoop.sh             |  15 +
 whole-genome-alignment/scripts/count_DNA.py   |  25 +
 .../{ => scripts}/create_jobs.sh              |   0
 whole-genome-alignment/scripts/lastz.sh       |  26 +
 .../scripts/lastz_commands.sh                 | 718 +++++++++++++++++
 .../scripts/maf-convert_commands.sh           | 718 +++++++++++++++++
 whole-genome-alignment/scripts/parse_FASTA.py |  24 +
 .../scripts/repeatMasker.sh                   |  18 +
 .../scripts/repeatMaskerCommands.sh           | 719 ++++++++++++++++++
 17 files changed, 4502 insertions(+)
 create mode 100644 whole-genome-alignment/.DS_Store
 create mode 100755 whole-genome-alignment/README.md
 create mode 100755 whole-genome-alignment/env/wga.yaml
 create mode 100755 whole-genome-alignment/scripts/alignment_QC.R
 create mode 100755 whole-genome-alignment/scripts/array_wrapper.slurm
 create mode 100755 whole-genome-alignment/scripts/axtChain_commands.sh
 create mode 100755 whole-genome-alignment/scripts/chainSort_commands.sh
 create mode 100755 whole-genome-alignment/scripts/changeFilenameLoop.sh
 create mode 100755 whole-genome-alignment/scripts/count_DNA.py
 rename whole-genome-alignment/{ => scripts}/create_jobs.sh (100%)
 create mode 100755 whole-genome-alignment/scripts/lastz.sh
 create mode 100755 whole-genome-alignment/scripts/lastz_commands.sh
 create mode 100755 whole-genome-alignment/scripts/maf-convert_commands.sh
 create mode 100755 whole-genome-alignment/scripts/parse_FASTA.py
 create mode 100755 whole-genome-alignment/scripts/repeatMasker.sh
 create mode 100755 whole-genome-alignment/scripts/repeatMaskerCommands.sh

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diff --git a/whole-genome-alignment/README.md b/whole-genome-alignment/README.md
new file mode 100755
index 0000000..459cccd
--- /dev/null
+++ b/whole-genome-alignment/README.md
@@ -0,0 +1,517 @@
+# Cross-species ChIPseq analysis
+
+## Notes on Whole Genome Alignment
+
+__Email from Camille Berthelot:__
+
+We have run into a similar problem with non-model species in a recent project.
+Here is the pipeline that we have had good success with, which is very similar to the conservation pipeline used by UCSC:
+
+- build a custom whole-genome alignment between the dunnart and mouse genomes with Lastz
+- produce the chains and nets for this alignment (e.g. hierarchical organisation of aligned regions to get a 1-to-1 alignment over the whole genomes)
+- use LiftOver to map your dunnart regions of interest to mouse (and reciprocally)
+
+We have benchmarked this pipeline against the one we used in the 20 mammals Cell paper, and there was almost no difference in the recovered regions.
+
+This however assumes that you have a good grip on bioinformatics and access to sufficient computational power, as building alignments is quite intensive. There are a number of online tutorials to build the alignment and nets using Lastz:
+http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto
+https://www.bioconductor.org/packages/release/bioc/vignettes/CNEr/inst/doc/PairwiseWholeGenomeAlignment.html
+https://github.com/hillerlab/GenomeAlignmentTools (more fine-tuned and advanced)
+
+__Methods from Hecker & Hiller 2020 Whole Genome Alignment:__
+Going to try this method.
+
+To compute pairwise and multiple genome alignments, we used the human hg38 assembly as the reference (Supplementary Fig. 1 shows the entire workflow). We first built pairwise alignments between human and a query species using lastz and axtChain to compute co-linear alignment chains [82]. To align placental mammals, we used previously determined lastz parameters (K = 2400, L = 3000, Y = 9400, H = 2000, and the lastz default scoring matrix) that have a sufficient sensitivity to capture orthologous exons [16]. To align chimpanzee, bonobo, and gorilla, we changed the lastz parameters (K = 4500 and L = 4500).
+
+After building chains, we applied RepeatFiller (RRID:SCR_017414), a method that performs another round of local alignment, considering unaligning regions ≤20 kb in size that are bounded by co-linear alignment blocks up- and downstream. RepeatFiller removes any repeat masking from the unaligned region and is therefore able to detect novel alignments between repetitive regions. We have previously shown that RepeatFiller detects several megabases of aligning repetitive sequences that would be missed otherwise. After RepeatFiller, we applied chainCleaner with parameters -LRfoldThreshold = 2.5 -doPairs -LRfoldThresholdPairs = 10 -maxPairDistance = 10000 -maxSuspectScore = 100000 -minBrokenChainScore = 75000 to improve alignment specificity. Pairwise alignment chains were converted into alignment nets using a modified version of chainNet that computes real scores of partial nets. Nets were filtered using NetFilterNonNested.perl with parameters -doUCSCSynFilter -keepSynNetsWithScore 5000 -keepInvNetsWithScore 5000, which applies the UCSC “syntenic net” score thresholds (minTopScore of 300000 and minSynScore of 200000) and keeps nested nets that align to the same locus (inversions or local translocations; net type “inv” or “syn” according to netClass) if they score ≥5,000. For the Mongolian gerbil, tarsier, Malayan flying lemur, sperm whale, Przewalski's horse, Weddell seal, Malayan pangolin, Chinese pangolin, Hoffmann's two-fingered sloth, and Cape rock hyrax that have genome assemblies with a scaffold N50 ≤1,000,000 and a contig N50 ≤100,000, we just required that nets have a score ≥100,000. For marsupials and platypus, we lowered the score threshold for nets to 10,000 and kept inv or syn nets with scores ≥3,000.
+
+### Some definitions
+
+In chain and net lingo, the __target__ is the reference genome sequence and the __query__ is some other genome sequence. For example, if you are viewing Human-Mouse alignments in the Human genome browser, human is the target and mouse is the query.
+
+A __gapless block__ is a base-for-base alignment between part of the target and part of the query, possibly including mismatching bases. It has the same length in bases on the target and the query. This is the output of the most primitive alignment algorithms.
+
+A __gap__ is a link between two gapless blocks, indicating that the target or the query has sequence that should be skipped over in order to make the best-scoring alignment. In other words, the scoring penalty for skipping over one or more bases is less than the penalty for continuing to align the sequences without skipping.
+
+A __single-sided gap__ is a gap in which sequence in either target or query must be skipped over. A plausible explanation for needing to skip over a base in the target while not skipping a base in the query is that either the target has an inserted base or the query has a deleted base. Many alignment tools produce alignments with single-sided gaps between gapless blocks.
+
+A __double-sided gap__ skips over sequence in both target and query because the sum of penalties for mismatching bases exceeds the penalty for extending a gap across them. This is possible only when the penalty for extending a gap is less than the penalty for creating a new gap and less than the penalty for a mismatch, and when the alignment algorithm is capable of considering double-sided gaps.
+
+A __chain__ is a sequence of non-overlapping gapless blocks, with single- or double-sided gaps between blocks. Within a chain, target and query coords are monotonically non-decreasing (i.e. always increasing or flat). Chains are constructed by the axtChain program which finds pairwise alignments with the same target and query sequence, on the same strand, that can be merged if overlapping and joined into one longer alignment with a higher score under an affine gap-scoring system (progressively decreasing penalties for longer gaps).
+
+* double-sided gaps are a new capability (blastz can't do that) that allow extremely long chains to be constructed.
+* not just orthologs, but paralogs too, can result in good chains. but that's useful!
+* chains should be symmetrical -- e.g. swap human-mouse -> mouse-human chains, and you should get approx. the same chains as if you chain swapped mouse-human blastz alignments. However, Blastz's dynamic masking is asymmetrical, so in practice those results are not exactly symmetrical. Also, dynamic masking in conjunction with changed chunk sizes can cause differences in results from one run to the next.
+* chained blastz alignments are not single-coverage in either target or query unless some subsequent filtering (like netting) is done.
+* chain tracks can contain massive pileups when a piece of the target aligns well to many places in the query. Common causes of this include insufficient masking of repeats and high-copy-number genes (or paralogs).
+
+A __net__ is a hierarchical collection of chains, with the highest-scoring non-overlapping chains on top, and their gaps filled in where possible by lower-scoring chains, which in turn may have gaps filled in by lower-level chains and so on.
+
+* I think a chain's qName also helps to determine which level it lands in, i.e. it makes a difference whether a chain's qName is the same as the top-level chain's qName or not, because the levels have meanings associated with them -- see details page.
+* a net is single-coverage for target but not for query, unless it has been filtered to be single-coverage on both target and query. By convention we add "rbest" to the net filename in that case.
+* because it's single-coverage in the target, it's no longer symmetrical.
+* the netter has two outputs, one of which we usually ignore: the target-centric net in query coordinates. The reciprocal best process uses that output: the query-referenced (but target-centric / target single-cov) net is turned back into component chains, and then those are netted to get single coverage in the query too; the two outputs of that netting are reciprocal-best in query and target coords. Reciprocal-best nets are symmetrical again.
+* nets do a good job of filtering out massive pileups by collapsing them down to (usually) a single level.
+* "LiftOver chains" are actually chains extracted from nets, or chains filtered by the netting process.
+
+
+### Preparation
+
+Spartan modules
+
+```
+module load foss
+module load lastz
+module load ucsc/21072020
+module load perl
+
+```
+
+#### Repeat mask dunnart genome
+
+Create conda environment will all the dependencies:
+
+```
+conda create -n wga
+conda activate wga
+conda config --add channels conda-forge
+conda config --add channels biocore
+conda config --add channels bioconda
+conda install repeatmasker
+```
+
+Run RepeatModeler to de novo find repeat regions in the dunnart genome:
+```
+BuildDatabase -name dunnart -engine ncbi Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta
+
+nohup RepeatModeler -database dunnart -pa 20 >& repeatmodeler.out
+
+```
+
+Run RepeatMasker to mask repeats in dunnart genome (makes repeats lowercase). Run as an array for scaffolds to make it quicker.
+Create commands for array slurm script: `repeatMasker.sh`
+
+```
+RepeatMasker -q -xsmall Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+```
+
+
+RepeatMasker -qq -xsmall Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta -lib /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/wholeGenomeAlignment/repeatModeler/consensi.fa -trf_prgm /home/lecook/.conda/envs/wga/bin/trf
+
+#### Split into scaffolds
+
+Using faSplit from the UCSC Kent Tools
+
+```
+faSplit byName Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta smiCra1/
+```
+
+
+#### Create .2bit and .sizes files
+
+```
+faToTwoBit ../../dunnart/genomes/Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr_RM.fasta smiCra1.2bit
+```
+
+```
+twoBitInfo smiCra1.2bit stdout | sort -k2rn > smiCra1.chrom.sizes
+```
+
+#### mm10 target genome
+http://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/mm10.2bit
+
+__mm10.2bit__ - contains the complete mouse/mm10 genome sequence in the 2bit file format.  Repeats from __RepeatMasker__ and __Tandem Repeats Finder__ (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.  
+
+
+### lastZ
+
+To align placental mammals, we used previously determined lastz parameters (K = 2400, L = 3000, Y = 9400, H = 2000, and the lastz default scoring matrix) that have a sufficient sensitivity to capture orthologous exons
+
+To align placental mammals, we used the lastz alignment parameters K = 2400, L = 3000, Y = 9400, H = 2000 and the lastz default scoring matrix, correspond- ing to parameter set 2 in Table 1. To align vertebrates, we used K = 2400, L = 3000, Y = 3400, H = 2000 and the HoxD55 scoring matrix. Citation: Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. Nucleic Acids Res. 2017;45(14):8369–77.
+
+Create commands for running lastZ for all scaffolds: `lastz.sh`
+
+Repeated with vertebrate alignment parameters and HoxD55 scoring matrix. Retrieve A LOT more aligned sequences. For example scaffold00002 with mammal parameters retrieved 863M of data, while with the new parameters it's 2.5GB.
+
+Run as an array on slurm: `array_wrapper.slurm`
+
+
+#### Convert maf to axt-format
+http://last.cbrc.jp/doc/maf-convert.html
+
+```
+module load last/last/1066
+maf-convert axt ${tr}.maf > ${tr}.axt
+```
+
+### axtChain
+
+We use axtChain (http://www.soe.ucsc.edu/~kent; default parameters) to build co-linear alignment chains.
+
+```
+axtChain -linearGap=loose -scoreScheme=../../bin/GenomeAlignmentTools/HoxD55.q mm10_smiCra1.axt mm10.2bit smiCra1.2bit mm10_smiCra1.chain
+```
+
+axtChain on psl alignments (patchChain new alignments plus genomeWide lastz alignments)
+
+```
+axtChain -psl -linearGap=loose -scoreScheme=../../bin/GenomeAlignmentTools/HoxD55.q all.psl ../../data/genomes/mm10.2bit ../../data/genomes/smiCra1.2bit smiCra1_mm10_patched.chain
+```
+
+4.7G Jan 31 18:42 smiCra1_mm10.chain
+5.3G Feb  1 17:52 smiCra1_mm10_patched.chain
+
+
+### chainMergeSort
+Merge short chains into longer ones, concatenate chains and sort
+
+```
+chainMergeSort *.chain > smiCra1_mm10.chain
+```
+
+__directory:__ /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/wholeGenomeAlignment/chainMerge/smiCra1_mm10.chain
+
+
+### Installing Genomic Alignment Tools (Hiller group)
+
+```
+git clone https://github.com/hillerlab/GenomeAlignmentTools.git
+
+cd GenomeAlignmentTools/kent/src
+
+make
+
+# Kent binaries
+PATH=$PATH:/Users/lauracook/bin/GenomeAlignmentTools/kent/bin;export PATH
+
+export KENTSRC_DIR=/Users/lauracook/bin/GenomeAlignmentTools/kent/src/
+
+cd /Users/lauracook/bin/GenomeAlignmentTools/src
+export MACHTYPE=x86_64
+make 
+
+PATH=$PATH:/Users/lauracook/bin/GenomeAlignmentTools/src
+
+```
+
+
+
+### RepeatFiller
+
+https://github.com/hillerlab/GenomeAlignmentTools
+
+RepeatFiller [5] is a tool to incorporate newly-detected repeat-overlapping alignments into pairwise alignment chains [4]. Its runtime adds little to the computationally more expensive step of generating chains in pairwise whole-genome alignments. RepeatFiller circumvents the problem that considering all repeat-overlapping alignment seeds during whole genome alignment is computationally not feasible. Therefore, RepeatFiller only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in the chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. RepeatFiller application to mammalian genome alignment chains can add between 22 and 84 Mb of previously-undetected alignments that mostly originate from transposable elements [5]. This helps to comprehensively align repetitive regions and improves the annotation of conserved non-coding elements.
+
+```
+python3 RepeatFiller.py -c smiCra1_mm10.chain -T2 mm10.2bit -Q2 smiCra1.2bit
+
+python3 RepeatFiller.py -c smiCra1_mm10_patched_sorted.chain -T2 ../../data/genomes/mm10.2bit -Q2 ../../data/genomes/smiCra1.2bit
+
+```
+RepeatFiller adds 0.3G data to the alignment - 2 Feb 2021
+
+
+__directory:__ /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/wholeGenomeAlignment/repeatFiller/
+
+
+### patchChain
+
+patchChain.perl performs a highly sensitive local pairwise alignment for loci flanked by aligning blocks [1,3]. Given an alignment chain [4], it considers all chains that pass the score and span filters (optional parameters), extracts all the unaligning loci and creates local alignment jobs. After executing these alignment jobs, the newly found and the original local alignments are combined and used to produce a new set of improved chains.
+
+This procedure is recommended for comparisons between species that are separated by >0.75 substitutions per neutral site [1].
+
+```
+patchChain.perl smiCra1_mm10.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.chrom.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.chrom.sizes -chainMinScore 5000 -gapMaxSizeT 500000 -gapMaxSizeQ 500000 -gapMinSizeT 30 -gapMinSizeQ 30 -numJobs 10 -jobDir jobs -jobList jobList -outputDir pslOutput -minEntropy 1.8 -windowSize 30 -minIdentity 60 -lastzParameters "--format=axt K=1500 L=2500 M=0 T=0 W=5 Q=/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/bin/GenomeAlignmentTools/example/HoxD55.q"
+```
+
+```
+this results in 10 alignment jobs that are located in jobs/ and listed in 'jobList'
+now execute these jobs on a compute cluster or run them sequentially by doing 'chmod +x jobList; ./jobList'
+
+# concatenate all new results
+find pslOutput -name "*.psl" | xargs -i cat {} > newAlignments.psl
+
+# concatenate all genomewide psl lastz alignments
+find psl -name "*.psl" | xargs -i cat {} > genomeWide.lastz.psl
+
+# combine the genome-wide lastz results (the combined psl file that was used to create the input chains) and the newly found psl alignments
+cat psl/genomeWide.lastz.psl patchChain/newAlignments.psl > all.psl 
+
+patchChain adds 1.1G to the genome wide alignment file
+
+# use axtChain from the Kent source to compute alignment chains that include the new alignments
+
+
+```
+
+
+This create a folder with the jobs and a jobList which can be called in an array slurm script. Then you can run the jobs in parallel.
+
+
+### chainCleaner
+
+https://github.com/hillerlab/GenomeAlignmentTools
+
+After RepeatFiller, we applied chainCleaner with parameters -LRfoldThreshold = 2.5 -doPairs -LRfoldThresholdPairs = 10 -maxPairDistance = 10000 -maxSuspectScore = 100000 -minBrokenChainScore = 75000 to improve alignment specificity.
+
+chainCleaner improves the specificity in genome alignment chains by detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements [2]. The input is a chain file, ideally after adding alignments found with highly sensitive parameters if distal species are compared. The output is a chain file that contains re-scored and score-sorted chains after removing the local alignments from the parent chains and adding them as individual chains. The resulting output file can be used to get alignment nets by running chainNet [4].
+
+
+```
+chainCleaner smiCra1_mm10_repFil.chain mm10.2bit smiCra1.2bit smiCra1_mm10_repFill_chainCl.chain smiCra1_mm10_repFill_chainCl.bed -tSizes=mm10.chrom.sizes -qSizes=smiCra1.chrom.sizes -LRfoldThreshold=2.5 -doPairs -LRfoldThresholdPairs=10 -maxPairDistance=10000 -maxSuspectScore=100000 -minBrokenChainScore=75000 -linearGap=loose
+```
+
+Run chain cleaner on patched chain file
+```
+chainCleaner smiCra1_mm10_patched_sorted_repFil.chain ../../data/genomes/mm10.2bit ../../data/genomes/smiCra1.2bit smiCra1_mm10_patched_sorted_repFil_chainCl.chain smiCra1_mm10_patched_sorted_repFil_chainCl.bed -tSizes=../../data/genomes/mm10.sizes -qSizes=../../data/genomes/smiCra1.sizes -LRfoldThreshold=2.5 -doPairs -LRfoldThresholdPairs=10 -maxPairDistance=10000 -maxSuspectScore=100000 -minBrokenChainScore=75000 -linearGap=loose
+```
+
+
+`-LRfoldThreshold` = threshold for removing local alignment blocks if the score of the left and right fill of brokenChain. Default is 2.5
+`-doPairs` = flag: if set, do test if pairs of chain breaking alignments can be removed
+`-LRfoldThresholdPairs` = threshold for removing local alignment blocks if the score of the left and right fill of broken chains (for pairs). Default = 10
+`-maxPairDistance` = only consider pairs of chain breaking alignments where the distance between the end of the upstream CBA and the start of the downstream CBA is at most that many bp (default 10000)
+`-maxSuspectScore` = threshold for score of suspect subChain. If higher, do not remove suspect.
+
+`-linearGap`=loose
+
+__directory:__ /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/wholeGenomeAlignment/chainCleaner/
+
+
+For filtering the chains, we need the size of each chromosome
+```
+faSize /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.fa -detailed > smiCra1.sizes
+faSize /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa -detailed > mm10.sizes
+```
+
+### chainPreNet
+
+```
+chainPreNet smiCra1_mm10_patched_sorted_chainCl.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes smiCra1_mm10_patched_sorted_chainCl.chain
+```
+
+chainPreNet without chainCleaner
+
+```
+chainPreNet smiCra1_mm10_patched_sorted_repFil_chainCl.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes smiCra1_mm10_patched_sorted_repFil_chainCl_preNet.chain
+```
+
+### chainNet
+Given a set of alignment chains, chainNet produces alignment nets, which is a hierarchical collection of chains or parts of chains that attempt to capture only orthologous alignments [4]. The original chainNet implementation approximates the score of "sub-nets" (nets that come from a part of a chain and fill a gap in a higher-level net) by the fraction of aligning bases. This can lead to a bias in case the aligning blocks of a chain are not equally distributed. We implemented a new parameter "-rescore" in chainNet that computes the real score of each subnet [2].
+
+Make the alignment nets:
+
+```
+chainNet smiCra1_mm10_patched_sorted_repFil_chainCl_preNet.chain -minSpace=1 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes stdout /dev/null | netSyntenic stdin smiCra1_mm10_patched_sorted_repFil_chainCl_preNet.net
+```
+
+```
+chainNet smiCra1_mm10_patched_sorted_chainCl.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes stdout /dev/null | netSyntenic stdin noClass.net
+chainNet smiCra1_mm10_patched_sorted_chainCl.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes mm10.net smiCra1.net
+
+chainNet smiCra1_mm10_patched_sorted_chainCl_preNet.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes stdout /dev/null | netSyntenic stdin noClass_pre.net
+chainNet smiCra1_mm10_patched_sorted_chainCl_preNet.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes mm10_pre.net smiCra1_pre.net
+
+chainNet smiCra1_mm10_patched_preNet.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes stdout /dev/null | netSyntenic stdin smiCra1_mm10_patched_preNet.chain.net
+
+```
+
+
+
+
+### netChainSubset
+Creates a single chain file using only the chains that also appear in the net.
+
+```
+netChainSubset mm10.smiCra1.net ../chainCleaner/smiCra1_mm10_repFill_chainCl.chain net.mm10.smiCra1.chain
+
+
+netChainSubset mm10.smiCra1.net ../chainCleaner/smiCra1_mm10_patched_sorted_chainCl.chain smiCra1_mm10_patched_sorted_chainCl_netted.chain -gapOut=gap.tab -wholeChains
+
+netChainSubset smiCra1_mm10_patched_sorted_repFil_chainCl_preNet.net ../chainCleaner/smiCra1_mm10_patched_sorted_repFil_chainCl.chain smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet.chain
+
+```
+
+
+### Join chain fragments
+```
+chainStitchId smiCra1_mm10_patched_sorted_chainCl_netted.chain smiCra1_mm10_patched_sorted_chainCl_netted_stitched.chain
+
+chainStitchId smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet.chain smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain
+
+```
+
+
+From the synteny files (positions), get the sequences and re-create alignments.
+
+### Create MAF files
+
+smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain
+
+```
+netToAxt chainNet/smiCra1_mm10_patched_sorted_repFil_chainCl_preNet.net liftOver_chains/smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit stdout | axtSort stdin mm10-smiCra1.axt
+
+axtToMaf netToAxt/mm10-smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.sizes /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.sizes mm10-smiCra1.maf -tPrefix=mm10. -qPrefix=smiCra1.
+```
+
+### chainSwap
+
+```
+chainSwap mm10_to_smiCra1_patched_sorted_chainCl_netted_stitched.chain stdout | nice chainSort stdin stdout | nice gzip -c > smiCra1_to_mm10_patched_sorted_chainCl_netted_stitched.chain
+
+chainSwap smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain stdout | nice chainSort stdin stdout > mm10_smiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain
+```
+
+### Quality control 
+
+MafFilter.
+Using mm10-smiCra1 maf file generated using axtToMaf look at the block lengths and genomic coverage.
+
+```
+maffilter param=options-file
+```
+
+Parameter options file
+```
+DATA=mm10-smiCra1 //A user-defined variable, representing the input maf file, without extension
+input.file=$(DATA).maf.gz  //Input maf file, gzipped
+input.file.compression=gzip
+output.log=$(DATA).maffilter.log //Output log file
+maf.filter=                                 \
+    SequenceStatistics(                     \
+        statistics=(                        \
+                BlockLength,                \
+            AlnScore,                       \
+            BlockCounts,                    \
+            PairwiseDivergence(             \
+                species1=mm10,              \
+                species2=smiCra1)),         \
+        ref_species=mm10,                   \
+        file=divergence.statistics.csv) 
+```
+
+Summarise block lengths, block counts, pairwise divergence and calculate exon coverage in the maf file between species in R = `alignment_QC.R`
+
+
+- Fraction of genomes aligned
+Simply calculate the number of base pairs (from MAF file)) to the number of total bp in the genome
+
+Dunnart to mouse
+
+Mouse to dunnart
+
+- Fraction of mouse exons are in the alignment, and what fraction you actually recover by using liftover.
+
+mm10 exons from refseq (downloaded from UCSC)
+
+dunnart exons from lifted devil annotation gtf file converted to a bed file using BEDOPS `gtf2bed` function
+```
+gff2bed < Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr2.gff > dunnart_gff.bed
+less dunnart_gff.bed | grep "exon" > dunnart_exons.bed
+```
+
+In Rstudio: `alignment_QC.R'
+
+## LiftOver
+
+smiCra1exonsMerged.bed
+```
+liftOver smiCra1exonsMerged.bed mm10_smiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain smiCra1exonsMapped.txt smiCra1exonsUnmapped.txt
+```
+number of dunnart exons = 193182
+number of dunnart exons that can be mapped to mouse = 111693
+
+```
+liftOver mm10exonsMerged.bed smiCra1_mm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain mm10exonsMapped.txt mm10exonsUnmapped.txt
+```
+number of mouse exons = 193776
+number of mouse exons that can be lifted over to dunnart = 160213
+
+### Trim peaks to 100bp around the summit
+
+```
+# make list of peaks that overlap in both replicates
+less H3K4me3_overlap_sortedByPeak.narrowPeak | awk -F \t '{print $4}' | sort > H3K4me3_overlap_peaks.txt
+less H3K27ac_overlap.narrowPeak | awk -F \t '{print $4}' | sort > H3K27ac_overlap_peaks.txt
+
+# in R extract rows from summits file based on the list of peaks in overlap file for both H3K4me3 and H3K27ac
+summits <- read.table("H3K4me3_pooled_macs2_summits.bed")
+reps <- scan("H3K4me3_overlap_peaks.txt", what="", sep="\n")
+rep_summits <- subset(summits, V4 %in% reps)
+write.table(rep_summits, "H3K4me3_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
+
+# in bash use bedtools to extend the summits 50bp in both directions
+bedtools slop -i H3K4me3_overlap_summits.bed -b 50 -g smiCra1.chrom.sizes > H3K4me3_overlap_100bpsummits.bed
+bedtools slop -i H3K27ac_overlap_summits.bed -b 50 -g smiCra1.chrom.sizes > H3K27ac_overlap_100bpsummits.bed
+```
+
+# Whole genome alignment with new chromosome level assembly
+## Preparation
+
+Spartan modules
+
+```
+module load foss
+module load lastz
+module load ucsc/21072020
+module load perl
+conda activate wga
+
+```
+
+### Repeat mask dunnart genome
+
+
+Run RepeatModeler to de novo find repeat regions in the dunnart genome:
+```
+BuildDatabase -name dunnart -engine ncbi Sminthopsis_crassicaudata_HiC.fasta
+
+nohup RepeatModeler -database dunnart -pa 20 >& repeatmodeler.out
+
+```
+
+Run RepeatMasker to mask repeats in dunnart genome (makes repeats lowercase). Run as an array for scaffolds to make it quicker.
+Create commands for array slurm script: `repeatMaskerHiC.sh`
+
+Using faSplit from the UCSC Kent Tools to split into scaffolds
+
+```
+faSplit byName Sminthopsis_crassicaudata_HiC.fasta faSplit/
+```
+
+```
+RepeatMasker -q -xsmall smiCra1_HiC/*.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+```
+
+### Create .2bit and .sizes files
+
+```
+faToTwoBit Sminthopsis_crassicaudata_HiC.fasta smiCra1_HiC.2bit
+```
+
+```
+twoBitInfo smiCra1.2bit stdout | sort -k2rn > smiCra1.chrom.sizes
+```
+
+## Genome alignment with LASTZ
+Create commands for running lastZ for all scaffolds: `lastz.sh`
+
+Repeated with vertebrate alignment parameters and HoxD55 scoring matrix. Retrieve A LOT more aligned sequences. For example scaffold00002 with mammal parameters retrieved 863M of data, while with the new parameters it's 2.5GB.
+
+Run as an array on slurm: `array_wrapper.slurm`
+
+### References
+
+[1] Sharma V, Hiller M. Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. Nucleic Acids Res., 45(14), 8369–8377, 2017
+
+[2] Suarez H, Langer BE, Ladde P, Hiller M. chainCleaner improves genome alignment specificity and sensitivity. Bioinformatics, 33(11):1596-1603, 2017
+
+[3] Hiller M, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Res, 41(15):e151.
+
+[4] Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. PNAS, 100(20):11484-9, 2003
+
+[5] Osipova E, Hecker N, Hiller M. RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements, submitted
+
+[6] MafFilter
+
+[7] Kent tools UCSC
\ No newline at end of file
diff --git a/whole-genome-alignment/env/wga.yaml b/whole-genome-alignment/env/wga.yaml
new file mode 100755
index 0000000..96fbe71
--- /dev/null
+++ b/whole-genome-alignment/env/wga.yaml
@@ -0,0 +1,153 @@
+name: wga
+channels:
+  - bioconda
+  - biocore
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
+  - bzip2=1.0.8=h516909a_3
+  - c-ares=1.11.0=h470a237_1
+  - ca-certificates=2020.6.20=hecda079_0
+  - cairo=1.16.0=h3fc0475_1005
+  - cd-hit=4.8.1=h8b12597_3
+  - certifi=2020.6.20=py38h32f6830_0
+  - curl=7.71.1=he644dc0_6
+  - entrez-direct=13.9=pl526h375a9b1_0
+  - expat=2.2.9=he1b5a44_2
+  - fontconfig=2.13.1=h1056068_1002
+  - freetype=2.10.2=he06d7ca_0
+  - fribidi=1.0.10=h516909a_0
+  - genometools-genometools=1.6.1=py38h23571c4_2
+  - gettext=0.19.8.1=hc5be6a0_1002
+  - glib=2.66.0=h0dae87d_0
+  - gmp=6.1.2=hf484d3e_1000
+  - gnutls=3.5.19=h2a4e5f8_1
+  - graphite2=1.3.13=he1b5a44_1001
+  - harfbuzz=2.7.2=hee91db6_0
+  - hmmer=3.3.1=he1b5a44_0
+  - icu=67.1=he1b5a44_0
+  - krb5=1.17.1=hfafb76e_3
+  - ld_impl_linux-64=2.35=h769bd43_9
+  - libcurl=7.71.1=hcdd3856_6
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libffi=3.2.1=he1b5a44_1007
+  - libgcc-ng=9.3.0=h24d8f2e_16
+  - libgomp=9.3.0=h24d8f2e_16
+  - libiconv=1.16=h516909a_0
+  - libnghttp2=1.41.0=hab1572f_1
+  - libpng=1.6.37=hed695b0_2
+  - libssh2=1.9.0=hab1572f_5
+  - libstdcxx-ng=9.3.0=hdf63c60_16
+  - libuuid=2.32.1=h14c3975_1000
+  - libxcb=1.13=h14c3975_1002
+  - libxml2=2.9.10=h68273f3_2
+  - llvm-openmp=8.0.1=hc9558a2_0
+  - ltr_retriever=2.9.0=0
+  - mafft=7.471=h516909a_0
+  - ncurses=6.2=he1b5a44_1
+  - nettle=3.3=0
+  - nseg=1.0.1=h516909a_0
+  - openmp=8.0.1=0
+  - openssl=1.1.1h=h516909a_0
+  - pango=1.42.4=h7062337_4
+  - pcre=8.44=he1b5a44_0
+  - perl=5.26.2=h516909a_1006
+  - perl-app-cpanminus=1.7044=pl526_1
+  - perl-archive-tar=2.32=pl526_0
+  - perl-base=2.23=pl526_1
+  - perl-business-isbn=3.004=pl526_0
+  - perl-business-isbn-data=20140910.003=pl526_0
+  - perl-carp=1.38=pl526_3
+  - perl-common-sense=3.74=pl526_2
+  - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
+  - perl-compress-raw-zlib=2.087=pl526hc9558a2_0
+  - perl-constant=1.33=pl526_1
+  - perl-data-dumper=2.173=pl526_0
+  - perl-digest-hmac=1.03=pl526_3
+  - perl-digest-md5=2.55=pl526_0
+  - perl-encode=2.88=pl526_1
+  - perl-encode-locale=1.05=pl526_6
+  - perl-exporter=5.72=pl526_1
+  - perl-exporter-tiny=1.002001=pl526_0
+  - perl-extutils-makemaker=7.36=pl526_1
+  - perl-file-listing=6.04=pl526_1
+  - perl-file-path=2.16=pl526_0
+  - perl-file-temp=0.2304=pl526_2
+  - perl-file-which=1.23=pl526_0
+  - perl-html-parser=3.72=pl526h6bb024c_5
+  - perl-html-tagset=3.20=pl526_3
+  - perl-html-tree=5.07=pl526_1
+  - perl-http-cookies=6.04=pl526_0
+  - perl-http-daemon=6.01=pl526_1
+  - perl-http-date=6.02=pl526_3
+  - perl-http-message=6.18=pl526_0
+  - perl-http-negotiate=6.01=pl526_3
+  - perl-io-compress=2.087=pl526he1b5a44_0
+  - perl-io-html=1.001=pl526_2
+  - perl-io-socket-ssl=2.066=pl526_0
+  - perl-io-zlib=1.10=pl526_2
+  - perl-json=4.02=pl526_0
+  - perl-json-xs=2.34=pl526h6bb024c_3
+  - perl-libwww-perl=6.39=pl526_0
+  - perl-list-moreutils=0.428=pl526_1
+  - perl-list-moreutils-xs=0.428=pl526_0
+  - perl-lwp-mediatypes=6.04=pl526_0
+  - perl-lwp-protocol-https=6.07=pl526_4
+  - perl-mime-base64=3.15=pl526_1
+  - perl-mozilla-ca=20180117=pl526_1
+  - perl-net-http=6.19=pl526_0
+  - perl-net-ssleay=1.88=pl526h90d6eec_0
+  - perl-ntlm=1.09=pl526_4
+  - perl-parent=0.236=pl526_1
+  - perl-pathtools=3.75=pl526h14c3975_1
+  - perl-scalar-list-utils=1.52=pl526h516909a_0
+  - perl-socket=2.027=pl526_1
+  - perl-storable=3.15=pl526h14c3975_0
+  - perl-test-requiresinternet=0.05=pl526_0
+  - perl-text-soundex=3.05=pl526_1000
+  - perl-time-local=1.28=pl526_1
+  - perl-try-tiny=0.30=pl526_1
+  - perl-types-serialiser=1.0=pl526_2
+  - perl-uri=1.76=pl526_0
+  - perl-www-robotrules=6.02=pl526_3
+  - perl-xml-namespacesupport=1.12=pl526_0
+  - perl-xml-parser=2.44=pl526h4e0c4b3_7
+  - perl-xml-sax=1.02=pl526_0
+  - perl-xml-sax-base=1.09=pl526_0
+  - perl-xml-sax-expat=0.51=pl526_3
+  - perl-xml-simple=2.25=pl526_1
+  - perl-xsloader=0.24=pl526_0
+  - pip=20.2.3=py_0
+  - pixman=0.38.0=h516909a_1003
+  - pthread-stubs=0.4=h14c3975_1001
+  - python=3.8.5=h1103e12_8_cpython
+  - python_abi=3.8=1_cp38
+  - readline=8.0=he28a2e2_2
+  - recon=1.08=h516909a_2
+  - repeatmasker=4.1.0=pl526_0
+  - repeatmodeler=2.0.1=pl526_0
+  - repeatscout=1.0.6=h516909a_1
+  - rmblast=2.9.0=h2d02072_0
+  - setuptools=49.6.0=py38h32f6830_1
+  - sqlite=3.33.0=h4cf870e_0
+  - tk=8.6.10=hed695b0_0
+  - trf=4.09.1=h516909a_0
+  - wheel=0.35.1=pyh9f0ad1d_0
+  - xorg-kbproto=1.0.7=h14c3975_1002
+  - xorg-libice=1.0.10=h516909a_0
+  - xorg-libsm=1.2.3=h84519dc_1000
+  - xorg-libx11=1.6.12=h516909a_0
+  - xorg-libxau=1.0.9=h14c3975_0
+  - xorg-libxdmcp=1.1.3=h516909a_0
+  - xorg-libxext=1.3.4=h516909a_0
+  - xorg-libxrender=0.9.10=h516909a_1002
+  - xorg-renderproto=0.11.1=h14c3975_1002
+  - xorg-xextproto=7.3.0=h14c3975_1002
+  - xorg-xproto=7.0.31=h14c3975_1007
+  - xz=5.2.5=h516909a_1
+  - zlib=1.2.11=h516909a_1009
+prefix: /home/lecook/.conda/envs/wga
+
diff --git a/whole-genome-alignment/scripts/alignment_QC.R b/whole-genome-alignment/scripts/alignment_QC.R
new file mode 100755
index 0000000..36faf5a
--- /dev/null
+++ b/whole-genome-alignment/scripts/alignment_QC.R
@@ -0,0 +1,90 @@
+
+library(plyr)
+library(dplyr)
+library(data.table)
+if (!requireNamespace("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+
+BiocManager::install("biostrings")
+library(seqinr)
+library(Biostrings)
+
+setwd("/Users/lauracook/OneDrive - The University of Melbourne/PhD (2018-2021)/8-WholeGenomeAlignment/2-UCSC_hoxD55_alignment/1-UCSC_alignment_QC/2-MafFilter/")
+# Summarise statistics from MafFilter
+mm10 <- read.table("mm10.statistics.csv", header=TRUE, sep="\t") # read in table
+smiCra1 <- read.table("smiCra1.statistics.csv", header=TRUE, sep="\t") # read in table
+head(mm10) #check file has been imported correctly
+
+mm10ChrCount <- mm10 %>% count(Chr, sort=TRUE)#how many blocks per chromosome
+smiCra1ChrCount <- smiCra1 %>% count(Chr, sort=TRUE) #how many blocks per chromosome
+
+#total size (incl gaps) just use mouse as the statistics are the same
+size1to10bp <- mm10[which(mm10$BlockLength>=1 & mm10$BlockLength<=10),]
+size10to100bp <- mm10[which(mm10$BlockLength>=10 & mm10$BlockLength<=100),]
+size100to1kb <- mm10[which(mm10$BlockLength>=100 & mm10$BlockLength<=1000),]
+size1kbto10kb <- mm10[which(mm10$BlockLength>=1000 & mm10$BlockLength<=10000),]
+size10kbto100kb <- mm10[which(mm10$BlockLength>=10000 & mm10$BlockLength<=100000),]
+size100kbto1Mb <- mm10[which(mm10$BlockLength>=100000 & mm10$BlockLength<=1000000),]
+
+count(size1to10bp)
+count(size10to100bp)
+count(size100to1kb)
+count(size1kbto10kb)
+count(size10kbto100kb)
+count(size100kbto1Mb)
+
+sum(size1to10bp$BlockLength)
+sum(size10to100bp$BlockLength)
+sum(size100to1kb$BlockLength)
+sum(size1kbto10kb$BlockLength)
+sum(size10kbto100kb$BlockLength)
+sum(size100kbto1Mb$BlockLength)
+
+setwd("/Users/lauracook/OneDrive - The University of Melbourne/PhD (2018-2021)/8-WholeGenomeAlignment/2-UCSC_hoxD55_alignment/1-UCSC_alignment_QC/")
+
+# MOUSE exon coverage
+#mm10 refseq ncbi curated exons downloaded from ucsc
+system("bedtools sort -i mm10exons.bed > mm10exonsSorted.bed", intern=TRUE) ## sort by coordinates
+system("bedtools merge -i mm10exonsSorted.bed > mm10exonsMerged.bed", intern=TRUE) ## bedtools merge where transcripts are the same coordinates or within each other
+system("bedtools merge -i mm10_mafAlignment.bed > mm10_mafAlignmentMerged.bed", intern=TRUE) ## also merge the maf alignments from the liftOver
+system("bedtools intersect -a mm10exonsMerged.bed -b mm10_mafAlignmentBlocks.bed -wo > mm10exonOverlaps.bed", intern=TRUE) ## intersect exon coordinates with maf alignment file
+
+## calculate coverage 
+mm10exon <- read.table("mm10exonsMerged.bed") ## exon file
+mm10exon$length <- (mm10exon$V3 - mm10exon$V2) ## exon length in ncbi refseq 
+mm10overlaps <- read.table("mm10exonOverlaps.bed") ## overlap file
+dim(mm10overlaps) ## check file imported correctly
+sum(mm10overlaps$V10) ## 31776094bps of exons found in maf alignment
+sum(mm10exon$length) ## 34221920bps of exons in refseq mm10
+mm10exonCoverage <- sum(mm10overlaps$V10)/sum(mm10exon$length) ## converge alignment exon bps/total exon bps
+
+## DUNNART exon coverage 
+system("bedtools sort -i dunnart_exons.bed > dunnart_exonsSorted.bed", intern = TRUE) ## sort by coordinates
+system("bedtools merge -i dunnart_exonsSorted.bed > smiCra1exonsMerged.bed", intern = TRUE) ## bedtools merge where transcripts are the same coordinates or within each other
+system("bedtools merge -i smiCra1_mafAlignmentBlocksSorted.bed > smiCra1_mafAlignmentMerged.bed", intern = TRUE) ## also merge the maf alignments from the liftOver
+system("bedtools intersect -a smiCra1exonsMerged.bed -b smiCra1_mafAlignmentMerged.bed -wo > smiCra1_exonOverlaps.bed", intern=TRUE) ## intersect exon coordinates with maf alignment file
+smiCra1exon <- read.table("smiCra1exonsMerged.bed", sep="\t", header=FALSE) ## exon file
+dim(smiCra1exon) ## check file imported correctly
+smiCra1exon$length <- (smiCra1exon$V3 - smiCra1exon$V2)  ## exon length
+smiCra1overlaps <- read.table("smiCra1_exonOverlaps.bed", sep="\t", header=FALSE) ## exon overlaps with maf alignment file
+dim(smiCra1overlaps) ## check imported correctly
+sum(smiCra1exon$length) # 63502228
+sum(smiCra1overlaps$V7) # 43939135
+smiCra1exonCoverage <- sum(smiCra1overlaps$V7)/sum(smiCra1exon$length)
+
+## average sequence percentage mismatches for dunnart and mouse
+mm10 <- read.table("mm10.divergence.statistics.csv", header=TRUE, sep="\t")
+smiCra1 <- read.table("smiCra1.divergence.statistics.csv", header=TRUE, sep="\t")
+
+mean(mm10$Div.mm10.smiCra1)
+mean(smiCra1$Div.smiCra1.mm10)
+
+## Genome coverage
+readDNAStringSet("mm10_mafAlignment_nogaps.fasta") #number bp in alignment 743350114
+readDNAStringSet("smiCra1_mafAlignment_nogaps.fasta") #number bp in alignment 747935780
+
+mm10genomeSize <- 2652783500
+smiCra1genomeSize <-2838290115
+
+mm10coverage <- 743350114/mm10genomeSize
+smiCra1coveage <- 747935780/smiCra1genomeSize
diff --git a/whole-genome-alignment/scripts/array_wrapper.slurm b/whole-genome-alignment/scripts/array_wrapper.slurm
new file mode 100755
index 0000000..e350115
--- /dev/null
+++ b/whole-genome-alignment/scripts/array_wrapper.slurm
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+### Author: Laura E Cook, University of Melbourne, 22/01/2020
+### Last update: 07/02/2020
+### Purpose: basic array wrapper script
+
+# Array set up:
+#SBATCH --array=618-718
+
+# Partition for the job:
+
+# The project ID which this job should run under:
+#SBATCH -A punim0586
+
+# Maximum number of tasks/CPU cores used by the job:
+#SBATCH --mem=50000
+
+#SBATCH --partition mig
+
+# Send yourself an email when the job:
+# aborts abnormally (fails)
+#SBATCH --mail-type=FAIL
+# ends successfully
+#SBATCH --mail-type=END
+
+#SBATCH --mail-user=lecook@student.unimelb.edu.au
+
+# The maximum running time of the job in days-hours:mins:sec
+#SBATCH --time=50:00:00
+
+# The name of the job:
+#SBATCH --job-name=array
+
+# Output control:
+#SBATCH --error="/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/logs/lastz_%a.stderr"
+#SBATCH --output="/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/logs/lastz_%a.stdout"
+
+# Load modules:
+
+module load foss
+module load lastz
+conda activate wga
+
+# Run the simulations:
+command=`head -n $SLURM_ARRAY_TASK_ID /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/scripts/lastz_commands.sh | tail -n 1`
+echo "SLURM_ARRAY_TASK_ID: " $SLURM_ARRAY_TASK_ID
+echo $command
+eval $command
\ No newline at end of file
diff --git a/whole-genome-alignment/scripts/axtChain_commands.sh b/whole-genome-alignment/scripts/axtChain_commands.sh
new file mode 100755
index 0000000..27f4552
--- /dev/null
+++ b/whole-genome-alignment/scripts/axtChain_commands.sh
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+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00704_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00704_pilon_pilon_mm10.smiCra1.chain
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+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00714_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00714_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00715_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00715_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00716_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00716_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00717_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00717_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00718_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00718_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00719_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00719_pilon_pilon_mm10.smiCra1.chain
diff --git a/whole-genome-alignment/scripts/chainSort_commands.sh b/whole-genome-alignment/scripts/chainSort_commands.sh
new file mode 100755
index 0000000..5964d5f
--- /dev/null
+++ b/whole-genome-alignment/scripts/chainSort_commands.sh
@@ -0,0 +1,713 @@
+chainSort scaffold00001_pilon_pilon_mm10.smiCra1.chain > scaffold00001_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00002_pilon_pilon_mm10.smiCra1.chain > scaffold00002_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00003_pilon_pilon_mm10.smiCra1.chain > scaffold00003_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00004_pilon_pilon_mm10.smiCra1.chain > scaffold00004_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00005_pilon_pilon_mm10.smiCra1.chain > scaffold00005_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00006_pilon_pilon_mm10.smiCra1.chain > scaffold00006_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00007_pilon_pilon_mm10.smiCra1.chain > scaffold00007_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00008_pilon_pilon_mm10.smiCra1.chain > scaffold00008_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00009_pilon_pilon_mm10.smiCra1.chain > scaffold00009_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00010_pilon_pilon_mm10.smiCra1.chain > scaffold00010_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00011_pilon_pilon_mm10.smiCra1.chain > scaffold00011_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00012_pilon_pilon_mm10.smiCra1.chain > scaffold00012_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00013_pilon_pilon_mm10.smiCra1.chain > scaffold00013_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00014_pilon_pilon_mm10.smiCra1.chain > scaffold00014_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00016_pilon_pilon_mm10.smiCra1.chain > scaffold00016_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00017_pilon_pilon_mm10.smiCra1.chain > scaffold00017_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00018_pilon_pilon_mm10.smiCra1.chain > scaffold00018_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00019_pilon_pilon_mm10.smiCra1.chain > scaffold00019_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00020_pilon_pilon_mm10.smiCra1.chain > scaffold00020_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00021_pilon_pilon_mm10.smiCra1.chain > scaffold00021_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00022_pilon_pilon_mm10.smiCra1.chain > scaffold00022_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00023_pilon_pilon_mm10.smiCra1.chain > scaffold00023_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00024_pilon_pilon_mm10.smiCra1.chain > scaffold00024_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00025_pilon_pilon_mm10.smiCra1.chain > scaffold00025_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00026_pilon_pilon_mm10.smiCra1.chain > scaffold00026_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00027_pilon_pilon_mm10.smiCra1.chain > scaffold00027_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00028_pilon_pilon_mm10.smiCra1.chain > scaffold00028_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00029_pilon_pilon_mm10.smiCra1.chain > scaffold00029_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00030_pilon_pilon_mm10.smiCra1.chain > scaffold00030_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00031_pilon_pilon_mm10.smiCra1.chain > scaffold00031_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00032_pilon_pilon_mm10.smiCra1.chain > scaffold00032_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00033_pilon_pilon_mm10.smiCra1.chain > scaffold00033_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00034_pilon_pilon_mm10.smiCra1.chain > scaffold00034_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00035_pilon_pilon_mm10.smiCra1.chain > scaffold00035_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00036_pilon_pilon_mm10.smiCra1.chain > scaffold00036_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00037_pilon_pilon_mm10.smiCra1.chain > scaffold00037_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00038_pilon_pilon_mm10.smiCra1.chain > scaffold00038_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00039_pilon_pilon_mm10.smiCra1.chain > scaffold00039_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00040_pilon_pilon_mm10.smiCra1.chain > scaffold00040_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00041_pilon_pilon_mm10.smiCra1.chain > scaffold00041_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00042_pilon_pilon_mm10.smiCra1.chain > scaffold00042_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00043_pilon_pilon_mm10.smiCra1.chain > scaffold00043_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00044_pilon_pilon_mm10.smiCra1.chain > scaffold00044_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00045_pilon_pilon_mm10.smiCra1.chain > scaffold00045_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00046_pilon_pilon_mm10.smiCra1.chain > scaffold00046_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00047_pilon_pilon_mm10.smiCra1.chain > scaffold00047_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00048_pilon_pilon_mm10.smiCra1.chain > scaffold00048_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00049_pilon_pilon_mm10.smiCra1.chain > scaffold00049_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00050_pilon_pilon_mm10.smiCra1.chain > scaffold00050_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00051_pilon_pilon_mm10.smiCra1.chain > scaffold00051_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00052_pilon_pilon_mm10.smiCra1.chain > scaffold00052_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00053_pilon_pilon_mm10.smiCra1.chain > scaffold00053_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00054_pilon_pilon_mm10.smiCra1.chain > scaffold00054_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00055_pilon_pilon_mm10.smiCra1.chain > scaffold00055_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00056_pilon_pilon_mm10.smiCra1.chain > scaffold00056_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00057_pilon_pilon_mm10.smiCra1.chain > scaffold00057_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00058_pilon_pilon_mm10.smiCra1.chain > scaffold00058_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00059_pilon_pilon_mm10.smiCra1.chain > scaffold00059_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00060_pilon_pilon_mm10.smiCra1.chain > scaffold00060_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00061_pilon_pilon_mm10.smiCra1.chain > scaffold00061_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00062_pilon_pilon_mm10.smiCra1.chain > scaffold00062_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00063_pilon_pilon_mm10.smiCra1.chain > scaffold00063_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00064_pilon_pilon_mm10.smiCra1.chain > scaffold00064_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00065_pilon_pilon_mm10.smiCra1.chain > scaffold00065_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00066_pilon_pilon_mm10.smiCra1.chain > scaffold00066_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00067_pilon_pilon_mm10.smiCra1.chain > scaffold00067_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00068_pilon_pilon_mm10.smiCra1.chain > scaffold00068_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00069_pilon_pilon_mm10.smiCra1.chain > scaffold00069_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00070_pilon_pilon_mm10.smiCra1.chain > scaffold00070_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00071_pilon_pilon_mm10.smiCra1.chain > scaffold00071_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00072_pilon_pilon_mm10.smiCra1.chain > scaffold00072_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00073_pilon_pilon_mm10.smiCra1.chain > scaffold00073_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00074_pilon_pilon_mm10.smiCra1.chain > scaffold00074_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00075_pilon_pilon_mm10.smiCra1.chain > scaffold00075_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00076_pilon_pilon_mm10.smiCra1.chain > scaffold00076_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00077_pilon_pilon_mm10.smiCra1.chain > scaffold00077_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00078_pilon_pilon_mm10.smiCra1.chain > scaffold00078_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00079_pilon_pilon_mm10.smiCra1.chain > scaffold00079_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00080_pilon_pilon_mm10.smiCra1.chain > scaffold00080_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00081_pilon_pilon_mm10.smiCra1.chain > scaffold00081_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00082_pilon_pilon_mm10.smiCra1.chain > scaffold00082_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00083_pilon_pilon_mm10.smiCra1.chain > scaffold00083_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00084_pilon_pilon_mm10.smiCra1.chain > scaffold00084_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00085_pilon_pilon_mm10.smiCra1.chain > scaffold00085_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00086_pilon_pilon_mm10.smiCra1.chain > scaffold00086_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00087_pilon_pilon_mm10.smiCra1.chain > scaffold00087_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00088_pilon_pilon_mm10.smiCra1.chain > scaffold00088_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00089_pilon_pilon_mm10.smiCra1.chain > scaffold00089_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00090_pilon_pilon_mm10.smiCra1.chain > scaffold00090_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00091_pilon_pilon_mm10.smiCra1.chain > scaffold00091_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00092_pilon_pilon_mm10.smiCra1.chain > scaffold00092_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00093_pilon_pilon_mm10.smiCra1.chain > scaffold00093_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00094_pilon_pilon_mm10.smiCra1.chain > scaffold00094_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00095_pilon_pilon_mm10.smiCra1.chain > scaffold00095_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00096_pilon_pilon_mm10.smiCra1.chain > scaffold00096_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00097_pilon_pilon_mm10.smiCra1.chain > scaffold00097_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00098_pilon_pilon_mm10.smiCra1.chain > scaffold00098_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00099_pilon_pilon_mm10.smiCra1.chain > scaffold00099_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00100_pilon_pilon_mm10.smiCra1.chain > scaffold00100_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00101_pilon_pilon_mm10.smiCra1.chain > scaffold00101_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00102_pilon_pilon_mm10.smiCra1.chain > scaffold00102_pilon_pilon_mm10.smiCra1.sorted.chain
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+chainSort scaffold00626_pilon_pilon_mm10.smiCra1.chain > scaffold00626_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00627_pilon_pilon_mm10.smiCra1.chain > scaffold00627_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00628_pilon_pilon_mm10.smiCra1.chain > scaffold00628_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00629_pilon_pilon_mm10.smiCra1.chain > scaffold00629_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00630_pilon_pilon_mm10.smiCra1.chain > scaffold00630_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00631_pilon_pilon_mm10.smiCra1.chain > scaffold00631_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00632_pilon_pilon_mm10.smiCra1.chain > scaffold00632_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00633_pilon_pilon_mm10.smiCra1.chain > scaffold00633_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00634_pilon_pilon_mm10.smiCra1.chain > scaffold00634_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00635_pilon_pilon_mm10.smiCra1.chain > scaffold00635_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00636_pilon_pilon_mm10.smiCra1.chain > scaffold00636_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00637_pilon_pilon_mm10.smiCra1.chain > scaffold00637_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00638_pilon_pilon_mm10.smiCra1.chain > scaffold00638_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00639_pilon_pilon_mm10.smiCra1.chain > scaffold00639_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00640_pilon_pilon_mm10.smiCra1.chain > scaffold00640_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00641_pilon_pilon_mm10.smiCra1.chain > scaffold00641_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00642_pilon_pilon_mm10.smiCra1.chain > scaffold00642_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00643_pilon_pilon_mm10.smiCra1.chain > scaffold00643_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00644_pilon_pilon_mm10.smiCra1.chain > scaffold00644_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00645_pilon_pilon_mm10.smiCra1.chain > scaffold00645_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00646_pilon_pilon_mm10.smiCra1.chain > scaffold00646_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00647_pilon_pilon_mm10.smiCra1.chain > scaffold00647_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00648_pilon_pilon_mm10.smiCra1.chain > scaffold00648_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00649_pilon_pilon_mm10.smiCra1.chain > scaffold00649_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00650_pilon_pilon_mm10.smiCra1.chain > scaffold00650_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00651_pilon_pilon_mm10.smiCra1.chain > scaffold00651_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00652_pilon_pilon_mm10.smiCra1.chain > scaffold00652_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00653_pilon_pilon_mm10.smiCra1.chain > scaffold00653_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00654_pilon_pilon_mm10.smiCra1.chain > scaffold00654_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00655_pilon_pilon_mm10.smiCra1.chain > scaffold00655_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00656_pilon_pilon_mm10.smiCra1.chain > scaffold00656_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00657_pilon_pilon_mm10.smiCra1.chain > scaffold00657_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00658_pilon_pilon_mm10.smiCra1.chain > scaffold00658_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00659_pilon_pilon_mm10.smiCra1.chain > scaffold00659_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00660_pilon_pilon_mm10.smiCra1.chain > scaffold00660_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00661_pilon_pilon_mm10.smiCra1.chain > scaffold00661_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00662_pilon_pilon_mm10.smiCra1.chain > scaffold00662_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00663_pilon_pilon_mm10.smiCra1.chain > scaffold00663_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00664_pilon_pilon_mm10.smiCra1.chain > scaffold00664_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00665_pilon_pilon_mm10.smiCra1.chain > scaffold00665_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00666_pilon_pilon_mm10.smiCra1.chain > scaffold00666_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00667_pilon_pilon_mm10.smiCra1.chain > scaffold00667_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00668_pilon_pilon_mm10.smiCra1.chain > scaffold00668_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00669_pilon_pilon_mm10.smiCra1.chain > scaffold00669_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00670_pilon_pilon_mm10.smiCra1.chain > scaffold00670_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00671_pilon_pilon_mm10.smiCra1.chain > scaffold00671_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00672_pilon_pilon_mm10.smiCra1.chain > scaffold00672_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00673_pilon_pilon_mm10.smiCra1.chain > scaffold00673_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00674_pilon_pilon_mm10.smiCra1.chain > scaffold00674_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00675_pilon_pilon_mm10.smiCra1.chain > scaffold00675_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00676_pilon_pilon_mm10.smiCra1.chain > scaffold00676_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00677_pilon_pilon_mm10.smiCra1.chain > scaffold00677_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00678_pilon_pilon_mm10.smiCra1.chain > scaffold00678_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00679_pilon_pilon_mm10.smiCra1.chain > scaffold00679_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00680_pilon_pilon_mm10.smiCra1.chain > scaffold00680_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00681_pilon_pilon_mm10.smiCra1.chain > scaffold00681_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00682_pilon_pilon_mm10.smiCra1.chain > scaffold00682_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00683_pilon_pilon_mm10.smiCra1.chain > scaffold00683_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00684_pilon_pilon_mm10.smiCra1.chain > scaffold00684_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00685_pilon_pilon_mm10.smiCra1.chain > scaffold00685_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00686_pilon_pilon_mm10.smiCra1.chain > scaffold00686_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00687_pilon_pilon_mm10.smiCra1.chain > scaffold00687_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00688_pilon_pilon_mm10.smiCra1.chain > scaffold00688_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00689_pilon_pilon_mm10.smiCra1.chain > scaffold00689_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00690_pilon_pilon_mm10.smiCra1.chain > scaffold00690_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00691_pilon_pilon_mm10.smiCra1.chain > scaffold00691_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00692_pilon_pilon_mm10.smiCra1.chain > scaffold00692_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00693_pilon_pilon_mm10.smiCra1.chain > scaffold00693_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00694_pilon_pilon_mm10.smiCra1.chain > scaffold00694_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00695_pilon_pilon_mm10.smiCra1.chain > scaffold00695_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00696_pilon_pilon_mm10.smiCra1.chain > scaffold00696_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00697_pilon_pilon_mm10.smiCra1.chain > scaffold00697_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00698_pilon_pilon_mm10.smiCra1.chain > scaffold00698_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00699_pilon_pilon_mm10.smiCra1.chain > scaffold00699_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00700_pilon_pilon_mm10.smiCra1.chain > scaffold00700_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00701_pilon_pilon_mm10.smiCra1.chain > scaffold00701_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00702_pilon_pilon_mm10.smiCra1.chain > scaffold00702_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00703_pilon_pilon_mm10.smiCra1.chain > scaffold00703_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00704_pilon_pilon_mm10.smiCra1.chain > scaffold00704_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00705_pilon_pilon_mm10.smiCra1.chain > scaffold00705_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00706_pilon_pilon_mm10.smiCra1.chain > scaffold00706_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00707_pilon_pilon_mm10.smiCra1.chain > scaffold00707_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00708_pilon_pilon_mm10.smiCra1.chain > scaffold00708_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00709_pilon_pilon_mm10.smiCra1.chain > scaffold00709_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00710_pilon_pilon_mm10.smiCra1.chain > scaffold00710_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00711_pilon_pilon_mm10.smiCra1.chain > scaffold00711_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00712_pilon_pilon_mm10.smiCra1.chain > scaffold00712_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00713_pilon_pilon_mm10.smiCra1.chain > scaffold00713_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00714_pilon_pilon_mm10.smiCra1.chain > scaffold00714_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00715_pilon_pilon_mm10.smiCra1.chain > scaffold00715_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00716_pilon_pilon_mm10.smiCra1.chain > scaffold00716_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00717_pilon_pilon_mm10.smiCra1.chain > scaffold00717_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00718_pilon_pilon_mm10.smiCra1.chain > scaffold00718_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00719_pilon_pilon_mm10.smiCra1.chain > scaffold00719_pilon_pilon_mm10.smiCra1.sorted.chain
diff --git a/whole-genome-alignment/scripts/changeFilenameLoop.sh b/whole-genome-alignment/scripts/changeFilenameLoop.sh
new file mode 100755
index 0000000..e41606c
--- /dev/null
+++ b/whole-genome-alignment/scripts/changeFilenameLoop.sh
@@ -0,0 +1,15 @@
+##!/usr/bin/env bash
+
+## Change file names in a loop
+
+TRA=($(for file in *.fa.masked; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+mv ${tr}.fa.masked ${tr}.fa
+
+done
\ No newline at end of file
diff --git a/whole-genome-alignment/scripts/count_DNA.py b/whole-genome-alignment/scripts/count_DNA.py
new file mode 100755
index 0000000..5b37d64
--- /dev/null
+++ b/whole-genome-alignment/scripts/count_DNA.py
@@ -0,0 +1,25 @@
+#!usr/bin/env python3
+
+import string
+import random
+import sys
+import os
+from Bio import SeqIO
+
+
+file = sys.argv[1]
+
+# Loop through all the files in the variable
+with open(file, 'r') as fasta:
+
+    # for each record (TWAR header) in the file parse it as a FASTA
+    for record in SeqIO.parse(fasta, "fasta"):
+        # set each fasta to a seq
+        seq = record.seq
+        print("Count of A: ", seq.count("A"))
+        print("Count of C: ", seq.count("C"))
+        print("Count of G: ", seq.count("G"))
+        print("Count of T: ", seq.count("T"))
+fasta.close()
+
+#GCATGC
diff --git a/whole-genome-alignment/create_jobs.sh b/whole-genome-alignment/scripts/create_jobs.sh
similarity index 100%
rename from whole-genome-alignment/create_jobs.sh
rename to whole-genome-alignment/scripts/create_jobs.sh
diff --git a/whole-genome-alignment/scripts/lastz.sh b/whole-genome-alignment/scripts/lastz.sh
new file mode 100755
index 0000000..9017129
--- /dev/null
+++ b/whole-genome-alignment/scripts/lastz.sh
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+## This script loops through all scaffolds in the dunnart genome and
+## generates a separate command for each scaffold
+## These commands are then used in a slurm array script to run jobs in parallel
+
+TRA=($(for file in *.chain; do echo $file |cut -d "." -f 1-2;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+# generate lastz commands
+#echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/'${tr}.fa 'H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/'${tr}_mm10.smiCra1.maf
+
+# generate convert maf to axt format commands
+#echo 'maf-convert axt '${tr}.maf' > '${tr}.axt
+
+## build co-linear alignment chains
+#echo 'axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/'${tr}'.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit '${tr}'.chain'
+
+echo 'chainSort '${tr}'.chain > '${tr}'.sorted.chain'
+
+done
diff --git a/whole-genome-alignment/scripts/lastz_commands.sh b/whole-genome-alignment/scripts/lastz_commands.sh
new file mode 100755
index 0000000..a382934
--- /dev/null
+++ b/whole-genome-alignment/scripts/lastz_commands.sh
@@ -0,0 +1,718 @@
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00001_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00001_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00003_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00003_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00004_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00004_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00005_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00005_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00006_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00006_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00007_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00007_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00008_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00008_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00009_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00009_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00010_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00010_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00011_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00011_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00012_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00012_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00013_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00013_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00014_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00014_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00015_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00015_pilon_pilon_mm10.smiCra1.maf
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+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00718_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00718_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00719_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00719_pilon_pilon_mm10.smiCra1.maf
diff --git a/whole-genome-alignment/scripts/maf-convert_commands.sh b/whole-genome-alignment/scripts/maf-convert_commands.sh
new file mode 100755
index 0000000..cb33564
--- /dev/null
+++ b/whole-genome-alignment/scripts/maf-convert_commands.sh
@@ -0,0 +1,718 @@
+maf-convert axt scaffold00001_pilon_pilon_mm10.smiCra1.maf > scaffold00001_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00002_pilon_pilon_mm10.smiCra1.maf > scaffold00002_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00003_pilon_pilon_mm10.smiCra1.maf > scaffold00003_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00004_pilon_pilon_mm10.smiCra1.maf > scaffold00004_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00005_pilon_pilon_mm10.smiCra1.maf > scaffold00005_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00006_pilon_pilon_mm10.smiCra1.maf > scaffold00006_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00007_pilon_pilon_mm10.smiCra1.maf > scaffold00007_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00008_pilon_pilon_mm10.smiCra1.maf > scaffold00008_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00009_pilon_pilon_mm10.smiCra1.maf > scaffold00009_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00010_pilon_pilon_mm10.smiCra1.maf > scaffold00010_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00011_pilon_pilon_mm10.smiCra1.maf > scaffold00011_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00012_pilon_pilon_mm10.smiCra1.maf > scaffold00012_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00013_pilon_pilon_mm10.smiCra1.maf > scaffold00013_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00014_pilon_pilon_mm10.smiCra1.maf > scaffold00014_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00016_pilon_pilon_mm10.smiCra1.maf > scaffold00016_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00017_pilon_pilon_mm10.smiCra1.maf > scaffold00017_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00018_pilon_pilon_mm10.smiCra1.maf > scaffold00018_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00019_pilon_pilon_mm10.smiCra1.maf > scaffold00019_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00020_pilon_pilon_mm10.smiCra1.maf > scaffold00020_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00021_pilon_pilon_mm10.smiCra1.maf > scaffold00021_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00022_pilon_pilon_mm10.smiCra1.maf > scaffold00022_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00023_pilon_pilon_mm10.smiCra1.maf > scaffold00023_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00024_pilon_pilon_mm10.smiCra1.maf > scaffold00024_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00025_pilon_pilon_mm10.smiCra1.maf > scaffold00025_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00026_pilon_pilon_mm10.smiCra1.maf > scaffold00026_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00027_pilon_pilon_mm10.smiCra1.maf > scaffold00027_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00028_pilon_pilon_mm10.smiCra1.maf > scaffold00028_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00029_pilon_pilon_mm10.smiCra1.maf > scaffold00029_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00030_pilon_pilon_mm10.smiCra1.maf > scaffold00030_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00031_pilon_pilon_mm10.smiCra1.maf > scaffold00031_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00032_pilon_pilon_mm10.smiCra1.maf > scaffold00032_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00033_pilon_pilon_mm10.smiCra1.maf > scaffold00033_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00034_pilon_pilon_mm10.smiCra1.maf > scaffold00034_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00035_pilon_pilon_mm10.smiCra1.maf > scaffold00035_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00036_pilon_pilon_mm10.smiCra1.maf > scaffold00036_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00037_pilon_pilon_mm10.smiCra1.maf > scaffold00037_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00038_pilon_pilon_mm10.smiCra1.maf > scaffold00038_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00039_pilon_pilon_mm10.smiCra1.maf > scaffold00039_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00040_pilon_pilon_mm10.smiCra1.maf > scaffold00040_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00041_pilon_pilon_mm10.smiCra1.maf > scaffold00041_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00042_pilon_pilon_mm10.smiCra1.maf > scaffold00042_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00043_pilon_pilon_mm10.smiCra1.maf > scaffold00043_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00044_pilon_pilon_mm10.smiCra1.maf > scaffold00044_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00045_pilon_pilon_mm10.smiCra1.maf > scaffold00045_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00046_pilon_pilon_mm10.smiCra1.maf > scaffold00046_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00047_pilon_pilon_mm10.smiCra1.maf > scaffold00047_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00048_pilon_pilon_mm10.smiCra1.maf > scaffold00048_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00049_pilon_pilon_mm10.smiCra1.maf > scaffold00049_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00050_pilon_pilon_mm10.smiCra1.maf > scaffold00050_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00051_pilon_pilon_mm10.smiCra1.maf > scaffold00051_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00052_pilon_pilon_mm10.smiCra1.maf > scaffold00052_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00214_pilon_pilon_mm10.smiCra1.maf > scaffold00214_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00215_pilon_pilon_mm10.smiCra1.maf > scaffold00215_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00216_pilon_pilon_mm10.smiCra1.maf > scaffold00216_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00217_pilon_pilon_mm10.smiCra1.maf > scaffold00217_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00218_pilon_pilon_mm10.smiCra1.maf > scaffold00218_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00219_pilon_pilon_mm10.smiCra1.maf > scaffold00219_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00220_pilon_pilon_mm10.smiCra1.maf > scaffold00220_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00221_pilon_pilon_mm10.smiCra1.maf > scaffold00221_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00222_pilon_pilon_mm10.smiCra1.maf > scaffold00222_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00223_pilon_pilon_mm10.smiCra1.maf > scaffold00223_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00224_pilon_pilon_mm10.smiCra1.maf > scaffold00224_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00225_pilon_pilon_mm10.smiCra1.maf > scaffold00225_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00226_pilon_pilon_mm10.smiCra1.maf > scaffold00226_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00227_pilon_pilon_mm10.smiCra1.maf > scaffold00227_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00228_pilon_pilon_mm10.smiCra1.maf > scaffold00228_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00229_pilon_pilon_mm10.smiCra1.maf > scaffold00229_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00230_pilon_pilon_mm10.smiCra1.maf > scaffold00230_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00233_pilon_pilon_mm10.smiCra1.maf > scaffold00233_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00234_pilon_pilon_mm10.smiCra1.maf > scaffold00234_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00235_pilon_pilon_mm10.smiCra1.maf > scaffold00235_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00236_pilon_pilon_mm10.smiCra1.maf > scaffold00236_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00237_pilon_pilon_mm10.smiCra1.maf > scaffold00237_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00238_pilon_pilon_mm10.smiCra1.maf > scaffold00238_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00239_pilon_pilon_mm10.smiCra1.maf > scaffold00239_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00240_pilon_pilon_mm10.smiCra1.maf > scaffold00240_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00241_pilon_pilon_mm10.smiCra1.maf > scaffold00241_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00262_pilon_pilon_mm10.smiCra1.maf > scaffold00262_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00263_pilon_pilon_mm10.smiCra1.maf > scaffold00263_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00343_pilon_pilon_mm10.smiCra1.maf > scaffold00343_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00366_pilon_pilon_mm10.smiCra1.maf > scaffold00366_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00368_pilon_pilon_mm10.smiCra1.maf > scaffold00368_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00369_pilon_pilon_mm10.smiCra1.maf > scaffold00369_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00370_pilon_pilon_mm10.smiCra1.maf > scaffold00370_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00371_pilon_pilon_mm10.smiCra1.maf > scaffold00371_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00372_pilon_pilon_mm10.smiCra1.maf > scaffold00372_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00373_pilon_pilon_mm10.smiCra1.maf > scaffold00373_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00374_pilon_pilon_mm10.smiCra1.maf > scaffold00374_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00375_pilon_pilon_mm10.smiCra1.maf > scaffold00375_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00376_pilon_pilon_mm10.smiCra1.maf > scaffold00376_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00377_pilon_pilon_mm10.smiCra1.maf > scaffold00377_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00378_pilon_pilon_mm10.smiCra1.maf > scaffold00378_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00379_pilon_pilon_mm10.smiCra1.maf > scaffold00379_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00380_pilon_pilon_mm10.smiCra1.maf > scaffold00380_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00381_pilon_pilon_mm10.smiCra1.maf > scaffold00381_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00382_pilon_pilon_mm10.smiCra1.maf > scaffold00382_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00383_pilon_pilon_mm10.smiCra1.maf > scaffold00383_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00384_pilon_pilon_mm10.smiCra1.maf > scaffold00384_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00385_pilon_pilon_mm10.smiCra1.maf > scaffold00385_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00386_pilon_pilon_mm10.smiCra1.maf > scaffold00386_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00387_pilon_pilon_mm10.smiCra1.maf > scaffold00387_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00388_pilon_pilon_mm10.smiCra1.maf > scaffold00388_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00389_pilon_pilon_mm10.smiCra1.maf > scaffold00389_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00390_pilon_pilon_mm10.smiCra1.maf > scaffold00390_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00391_pilon_pilon_mm10.smiCra1.maf > scaffold00391_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00535_pilon_pilon_mm10.smiCra1.maf > scaffold00535_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00536_pilon_pilon_mm10.smiCra1.maf > scaffold00536_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00537_pilon_pilon_mm10.smiCra1.maf > scaffold00537_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00538_pilon_pilon_mm10.smiCra1.maf > scaffold00538_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00539_pilon_pilon_mm10.smiCra1.maf > scaffold00539_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00540_pilon_pilon_mm10.smiCra1.maf > scaffold00540_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00541_pilon_pilon_mm10.smiCra1.maf > scaffold00541_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00542_pilon_pilon_mm10.smiCra1.maf > scaffold00542_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00543_pilon_pilon_mm10.smiCra1.maf > scaffold00543_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00544_pilon_pilon_mm10.smiCra1.maf > scaffold00544_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00545_pilon_pilon_mm10.smiCra1.maf > scaffold00545_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00546_pilon_pilon_mm10.smiCra1.maf > scaffold00546_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00547_pilon_pilon_mm10.smiCra1.maf > scaffold00547_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00548_pilon_pilon_mm10.smiCra1.maf > scaffold00548_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00549_pilon_pilon_mm10.smiCra1.maf > scaffold00549_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00550_pilon_pilon_mm10.smiCra1.maf > scaffold00550_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00551_pilon_pilon_mm10.smiCra1.maf > scaffold00551_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00552_pilon_pilon_mm10.smiCra1.maf > scaffold00552_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00555_pilon_pilon_mm10.smiCra1.maf > scaffold00555_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00557_pilon_pilon_mm10.smiCra1.maf > scaffold00557_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00558_pilon_pilon_mm10.smiCra1.maf > scaffold00558_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00559_pilon_pilon_mm10.smiCra1.maf > scaffold00559_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00562_pilon_pilon_mm10.smiCra1.maf > scaffold00562_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00570_pilon_pilon_mm10.smiCra1.maf > scaffold00570_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00573_pilon_pilon_mm10.smiCra1.maf > scaffold00573_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00574_pilon_pilon_mm10.smiCra1.maf > scaffold00574_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00577_pilon_pilon_mm10.smiCra1.maf > scaffold00577_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00584_pilon_pilon_mm10.smiCra1.maf > scaffold00584_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00695_pilon_pilon_mm10.smiCra1.maf > scaffold00695_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00696_pilon_pilon_mm10.smiCra1.maf > scaffold00696_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00697_pilon_pilon_mm10.smiCra1.maf > scaffold00697_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00698_pilon_pilon_mm10.smiCra1.maf > scaffold00698_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00699_pilon_pilon_mm10.smiCra1.maf > scaffold00699_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00700_pilon_pilon_mm10.smiCra1.maf > scaffold00700_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00701_pilon_pilon_mm10.smiCra1.maf > scaffold00701_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00702_pilon_pilon_mm10.smiCra1.maf > scaffold00702_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00703_pilon_pilon_mm10.smiCra1.maf > scaffold00703_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00704_pilon_pilon_mm10.smiCra1.maf > scaffold00704_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00705_pilon_pilon_mm10.smiCra1.maf > scaffold00705_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00706_pilon_pilon_mm10.smiCra1.maf > scaffold00706_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00707_pilon_pilon_mm10.smiCra1.maf > scaffold00707_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00708_pilon_pilon_mm10.smiCra1.maf > scaffold00708_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00709_pilon_pilon_mm10.smiCra1.maf > scaffold00709_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00710_pilon_pilon_mm10.smiCra1.maf > scaffold00710_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00711_pilon_pilon_mm10.smiCra1.maf > scaffold00711_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00712_pilon_pilon_mm10.smiCra1.maf > scaffold00712_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00713_pilon_pilon_mm10.smiCra1.maf > scaffold00713_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00714_pilon_pilon_mm10.smiCra1.maf > scaffold00714_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00715_pilon_pilon_mm10.smiCra1.maf > scaffold00715_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00716_pilon_pilon_mm10.smiCra1.maf > scaffold00716_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00717_pilon_pilon_mm10.smiCra1.maf > scaffold00717_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00718_pilon_pilon_mm10.smiCra1.maf > scaffold00718_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00719_pilon_pilon_mm10.smiCra1.maf > scaffold00719_pilon_pilon_mm10.smiCra1.axt
diff --git a/whole-genome-alignment/scripts/parse_FASTA.py b/whole-genome-alignment/scripts/parse_FASTA.py
new file mode 100755
index 0000000..e6bde95
--- /dev/null
+++ b/whole-genome-alignment/scripts/parse_FASTA.py
@@ -0,0 +1,24 @@
+#!usr/bin/env python3
+
+import string
+import random
+import sys
+import os
+from Bio import SeqIO
+
+## usage python3 parse_FASTA.py [input.fasta] > [output.fasta]
+
+file = sys.argv[1]
+
+# Loop through all the files in the variable
+with open(file, 'r') as all_TWARs:
+
+    # for each record (TWAR header) in the file parse it as a FASTA
+    for record in SeqIO.parse(all_TWARs, "fasta"):
+        # set the record ID to a variable
+        id = record.id
+        # set the TWAR sequence to a variable
+        seq = record.seq
+
+        print(">" + str(id) + "\n" + str(seq) + "*")
+all_TWARs.close()
diff --git a/whole-genome-alignment/scripts/repeatMasker.sh b/whole-genome-alignment/scripts/repeatMasker.sh
new file mode 100755
index 0000000..fc918a4
--- /dev/null
+++ b/whole-genome-alignment/scripts/repeatMasker.sh
@@ -0,0 +1,18 @@
+##!/usr/bin/env bash
+
+## This script loops through all scaffolds in the dunnart genome and
+## generates a separate RepeatMasker command for each scaffold
+## These commands are then used in a slurm array script to run jobs in parallel
+
+TRA=($(for file in *.fa; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo 'RepeatMasker -q -xsmall smiCra1/'${tr}'.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/'
+
+
+done
diff --git a/whole-genome-alignment/scripts/repeatMaskerCommands.sh b/whole-genome-alignment/scripts/repeatMaskerCommands.sh
new file mode 100755
index 0000000..90af40b
--- /dev/null
+++ b/whole-genome-alignment/scripts/repeatMaskerCommands.sh
@@ -0,0 +1,719 @@
+RepeatMasker -q -xsmall smiCra1/scaffold00001_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00002_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00003_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00004_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00005_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00006_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00007_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00008_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00009_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00010_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00011_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00012_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00013_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00014_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00015_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00016_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00017_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00018_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00019_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00020_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00021_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00022_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00023_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00024_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00025_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00026_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00027_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00028_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00029_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00030_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00031_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00032_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00033_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00034_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00035_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00036_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00037_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00038_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00039_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00040_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00041_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00042_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00043_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00044_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00045_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00046_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00047_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00048_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00049_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00050_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00051_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00052_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00053_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00054_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00055_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00056_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00057_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00058_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00059_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00060_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00061_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00062_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00063_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00064_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00065_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00066_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00067_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00068_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00069_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00070_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00071_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
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-- 
GitLab