From a6ff34dddb7eaa3c4755bc1e7032cbaecab95bbd Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 30 Sep 2020 18:35:41 +0200
Subject: [PATCH] src/RNAseq.nf : no softclip and trim 1base at 5' and 3' end
by hisat
---
src/RNAseq.nf | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 97a95fe2..e1d9f872 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -289,6 +289,9 @@ hisat2 -x ${index_id} \
--un-conc-gz ${file_id}_notaligned_R%.fastq.gz \
--rna-strandness ${params.strand} \
--dta \
+ --no-softclip\
+ --trim3 1\
+ --trim5 1\
2> ${file_id}_genome.txt \
| samtools view -bS -F 4 - \
| samtools sort -@ ${task.cpus} -o ${file_id}.bam \
--
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