User:Kawaji/101105 CTSS

Purpose

CTSS (Cage Tag Starting Site) BED file from BAM file

Script

#/bin/sh

samtools view -uq ${MAPPING_QUALITY} ${BAM} \
| bamToBed -i stdin \
| awk 'BEGIN{OFS="\t"}{if($6=="+"){print $1,$2,$5}}' \
| sort -k1,1 -k2,2n \
| groupBy -i stdin -grp 1,2 -opCols 3 -ops count \
| awk 'BEGIN{OFS="\t"}{print $1,$2,$2+1,  $1":"$2".."$2+1",+"  ,$3,"+"}'

samtools view -uq ${MAPPING_QUALITY} ${BAM} \
| bamToBed -i stdin \
| awk 'BEGIN{OFS="\t"}{if($6=="-"){print $1,$3,$5}}' \
| sort -k1,1 -k2,2n \
| groupBy -i stdin -grp 1,2 -opCols 3 -ops count \
| awk 'BEGIN{OFS="\t"}{print $1,$2-1,$2,  $1":"$2-1".."$2",-"  ,$3,"-"}'