featureCounts.sh

#!/bin/bash

BAMPATH=.
RESULTPATH=.
GENESFILE=allRegions.SAF
STRANDENESS=1
THREADS=20

featureCounts -a $GENESFILE -F SAF  \
            -o /dev/stdout -O -s $STRANDENESS -Q 5 \
            -T $THREADS --minOverlap 50 --primary \
        --readExtension5 10 --readExtension3 10 --ignoreDup \
        -p -P -d 18 -D 10000 -B -C $BAMPATH/*bam \
| sed 1d \
| cut -f6- \
| paste ${GENESFILE%.SAF}.info  - \
| sed '1s/.\///g' \
| cut -f2- \
> $RESULTPATH/repCounts.tsv