From 366a0d558f804944db4063a1a121d8ad891d5154 Mon Sep 17 00:00:00 2001
From: cbedet1 <cecile.bedet@ens-lyon.fr>
Date: Fri, 4 Mar 2022 18:56:47 +0100
Subject: [PATCH] modif of gff file to correct the bug in htseq count (gtf
format)
---
src/RNAseq_cec.sh | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq_cec.sh b/src/RNAseq_cec.sh
index d112a66..fdb942d 100755
--- a/src/RNAseq_cec.sh
+++ b/src/RNAseq_cec.sh
@@ -1,7 +1,9 @@
+# grep WormBase c_elegans.PRJNA13758.WS278.annotations.gff3 > c_elegans.PRJNA13758.WS278.wormbase.gff3
+
./nextflow run src/RNAseq_cec.nf \
-profile psmn \
--fastq "subset/*_R{1,2}.fastq.gz" \
--cds_fasta "data/c_elegans.PRJNA13758.WS278.all_transcripts.fa" \
--genomic_fasta "data/c_elegans.PRJNA13758.WS278.genomic.fa" \
- --genomic_gff3 "data/c_elegans.PRJNA13758.WS278.annotations.gff3" \
+ --genomic_gff3 "data/c_elegans.PRJNA13758.WS278.wormbase.gff3" \
-resume
--
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