clean up

whole-genome-alignment/README.md

@@ -444,62 +444,6 @@ write.table(rep_summits, "H3K4me3_overlap_summits.bed", quote=FALSE, col.names=F
 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