From 3c9c7d4dde3c80928f115ead5a209ad5bcfd2ee9 Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Mon, 16 Mar 2020 10:51:06 -0500
Subject: [PATCH] Changed tag from 'gene_id' to 'gene_name'
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index e7ae998..e4427f6 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -401,9 +401,9 @@ process makeFeatureCounts {
script:
"""
if [ "${endsManual_featureCounts }" == "se" ]; then
- featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam;
+ featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -a ${gtf} -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
elif [ "${endsManual_featureCounts }" == "pe" ]; then
- featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -p -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam;
+ featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -p -a ${gtf} -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
fi;
Rscript calculateTPM.R --count "${repRID}.featureCounts";
"""
--
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