diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh index 98b93e572299a4f1054c37587dfde4397013a943..5d1a362da7f790c8dafb40218f83f5d78f3463aa 100644 --- a/genect_rnaseq/geneabundance.sh +++ b/genect_rnaseq/geneabundance.sh @@ -44,6 +44,7 @@ module load subread/1.6.1 export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH featureCounts -s $stranded -M --fraction -J --ignoreDup -T $NPROC -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam} + mkdir ${pair_id}_stringtie cd ${pair_id}_stringtie stringtie ../${sbam} -p $NPROC -G ${gtf} -B -e -o denovo.gtf -A ../${pair_id}.fpkm.txt