diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh index e763ef7c10a6e3ec2f595fd1deb97f99d435b1c7..39aad284f18c21a6c93f1e7c08ac479e893d1c74 100644 --- a/genect_rnaseq/geneabundance.sh +++ b/genect_rnaseq/geneabundance.sh @@ -38,7 +38,9 @@ then SLURM_CPUS_ON_NODE=64 fi source /etc/profile.d/modules.sh -module load subread/1.6.1 stringtie/1.3.2d-intel +module load subread/1.6.1 +export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH + featureCounts -s $stranded -M --fraction -J --ignoreDup -T $SLURM_CPUS_ON_NODE -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam} mkdir ${pair_id}_stringtie cd ${pair_id}_stringtie