first commit

cross_species_comparison/README.md

@@ -283,7 +283,8 @@ https://github.com/josiahseaman/FluentDNA
 
 
 
-References
+### 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
@@ -293,3 +294,7 @@ References
 [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] FluentDNA paper
+
+[7] Kent tools UCSC
\ No newline at end of file

cross_species_comparison/scripts/lastz.sh

-##!/usr/bin/env bash
+#!/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 *.axt; do echo $file |cut -d "." -f 1-2;done))
+TRA=($(for file in *.chain; do echo $file |cut -d "." -f 1-2;done))
 
 echo ${TRA[@]}
 
@@ -19,7 +19,8 @@ do
 #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 '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

mouse/README.md

@@ -243,38 +243,20 @@ therefore if amount that overlaps between each replicate divided by the length o
 
 # Consensus peaks and grouping into putative enhancers and promoters
 
-Separate overlapped replicate peak files:
-```
-less H3K27ac_overlap.narrowPeak| grep "A-3" > H3K27ac_overlap_repA.narrowPeak
-
-less H3K27ac_overlap.narrowPeak| grep "B-3" > H3K27ac_overlap_repB.narrowPeak
-
-less H3K4me3_overlap.narrowPeak| grep "A-2" > H3K4me3_overlap_repA.narrowPeak
-
-less H3K4me3_overlap.narrowPeak| grep "B-2" > H3K4me3_overlap_repB.narrowPeak
-```
-
-Keep only the intersected region:
-```
-bedtools intersect -a H3K27ac_overlap_repA.narrowPeak -b H3K27ac_overlap_repB.narrowPeak > H3K27ac_consensus.narrowPeak
-
-bedtools intersect -a H3K4me3_overlap_repA.narrowPeak -b H3K4me3_overlap_repB.narrowPeak > H3K4me3_consensus.narrowPeak
-```
-
 Find uniquely H3K4me3 sites (i.e. peaks that don't overlap with H3K27ac):
 
 ```
-bedtools intersect -v -a macs2/H3K4me3_consensus.narrowPeak -b macs2/H3K27ac_consensus.narrowPeak > H3K4me3_only.narrowPeak
+bedtools intersect -v -a H3K4me3_overlap.narrowPeak -b H3K27ac_overlap.narrowPeak > H3K4me3_only.narrowPeak
 ```
 
 Find unique H3K27ac sites (i.e. peaks that don't overlap with H3K4me3):
 ```
-bedtools intersect -v macs2/H3K27ac_consensus.narrowPeak -b macs2/H3K4me3_consensus.narrowPeak > H3K27ac_only.narrowPeak
+bedtools intersect -v -a H3K27ac_overlap.narrowPeak -b H3K4me3_overlap.narrowPeak > H3K27ac_only.narrowPeak
 ```
 
 Find peaks common between H3K27ac & H3K4me3 with a reciprocal overlap of at least 50%.
 ```
-bedtools intersect -f 0.5 -r -a macs2/H3K4me3_consensus.narrowPeak -b macs2/H3K27ac_consensus.narrowPeak > H3K4me3_and_H3K27ac.narrowPeak
+bedtools intersect -f 0.5 -r -a H3K4me3_only.narrowPeak -b H3K27ac_only.narrowPeak > H3K4me3_and_H3K27ac.narrowPeak
 ```