run_featureCounts.pbs

#!/bin/bash

#PBS -m ae
#PBS -l nodes=1:ppn=12

export PATH=/diazlab/shared/bin:$PATH

#human
annot="/diazlab/refs/Homo_sapiens/NCBI/build37.2/Annotation/Genes/genes_ercc.gtf"
#chimp
#annot="/diazlab/refs/Pan_troglodytes/NCBI/build3.1/Annotation/Genes/genes_ercc.gtf"
#baboon
#annot="/diazlab/refs/baboon/Annotation/papAnu2_ercc.gtf"
#john lncRNA
#annot=/diazlab/liuj/hbrain/bulk/lncRNA_pipeline_v3/polya/ensembl_75_polya_augment_stringent.v3_ercc.pnky.gtf
#TNC
#annot=/diazlab/refs/Homo_sapiens/NCBI/build37.2/Annotation/Genes/TNC.gtf

annot_id=human

cd $indr
infl=''
for f in $(ls $indr)
do
    if [ -f "${indr}${f}/accepted_hits.bam" ]
    then
	infl="${infl}${indr}${f}/accepted_hits.bam "
    fi
done 

featureCounts -T 12 -p -C -a ${annot} -o "${otdr}${fname}" $infl

grep ERCC- "${otdr}${fname}_${annot_id}.txt" > "${otdr}ERCC-${fname}.txt"
grep -v ERCC- "${otdr}${fname}_${annot_id}.txt" > "${otdr}${fname}-tmp"
mv -f "${otdr}${fname}-tmp" "${otdr}${fname}_${annot_id}.txt"
rm -f "${otdr}${fname}-tmp"