From a37b535cba86db20d813a29a56e69b834ea0a25a Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Sat, 2 May 2020 13:57:05 -0500 Subject: [PATCH] Fix featureCounts --- workflow/rna-seq.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 3047f84..6c6b116 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -822,10 +822,12 @@ process countData { echo "LOG: running countData on the data" >> ${repRID}.countData.err if [ "${ends}" == "se" ] then - featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err + featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err + #featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err elif [ "${ends}" == "pe" ] then - featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err + featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err + #featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err fi #Calculate TPM from the resulting countData table -- GitLab