Removing Mitochondrial hits is not consistent between replicate and pseudo replicates

[amirshams84]

---Removing Mit Hit for replicate

zcat AB2969-L1_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -nc > AB2969-L1_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv AB2969-L1_R1.trim.PE2SE.nodup.rm_chr.tmp.gz AB2969-L1_R1.trim.PE2SE.nodup.tagAlign.gz

---Not Removing Mit Hit for Pseudo Replicates

zcat AB2969-L1_R1.trim.PE2SE.nodup.bedpe.gz | shuf --random-source=AB2969-L1_R1.trim.PE2SE.nodup.bedpe.gz | split -d -l $((nlines)) - AB2969-L1_R1.trim.PE2SE.nodup.

awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "AB2969-L1_R1.trim.PE2SE.nodup.00" | gzip -nc > AB2969-L1_R1.trim.PE2SE.nodup.pr1.tagAlign.gz

rm -f AB2969-L1_R1.trim.PE2SE.nodup.00

awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "AB2969-L1_R1.trim.PE2SE.nodup.01" | gzip -nc > AB2969-L1_R1.trim.PE2SE.nodup.pr2.tagAlign.gz

rm -f AB2969-L1_R1.trim.PE2SE.nodup.01

[leepc12]

It looks like you are looking at old pipeline?

Pipeline no longer uses BEDPE to make pseudo replicates for paired end data sets. Please take a look at spr_tag_PE() in modules/postalign_bed.bds. It uses TAG-ALIGN to make pseudos.