From ba8ad15c995bebe7de8687422ed615a63d8e934e Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Mon, 28 Sep 2020 10:53:40 +0200
Subject: [PATCH] src/RNAseq.nf : correct hisat mapping

---
 results/.gitignore |  1 -
 src/RNAseq.nf      | 10 ++++++----
 2 files changed, 6 insertions(+), 5 deletions(-)
 delete mode 100644 results/.gitignore

diff --git a/results/.gitignore b/results/.gitignore
deleted file mode 100644
index 72e8ffc0..00000000
--- a/results/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-*
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 77886039..2b940d89 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -229,8 +229,9 @@ hisat2 -x ${index_id} \
        -1 ${fastq_filtred[0]} \
        -2 ${fastq_filtred[1]} \
        --un-conc-gz ${file_id}_notaligned_R%.fastq.gz \
-       --rna-strandness 'F' \
-       2> ${file_id}.txt \
+       --rna-strandness 'FR' \
+       --dta \
+       2> ${file_id}_genome.txt \
 | samtools view -bS -F 4 - \
 | samtools sort -@ ${task.cpus} -o ${file_id}.bam \
 && samtools index ${file_id}.bam
@@ -245,7 +246,7 @@ HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC;
                    HISAT_ALIGNED_DEDUP}
 
 
-/* Fastqc of filtred reads */
+/* Fastqc of genome reads */
 
 process fastqc_genome {
   tag "$file_id"
@@ -401,7 +402,8 @@ hisat2 -x ${index2_id} \
        -p ${task.cpus} \
        -1 ${fastq_unaligned[0]} \
        -2 ${fastq_unaligned[1]} \
-       --rna-strandness 'F' \
+       --rna-strandness 'FR' \
+       --dta\
        2> ${file_id}_postgenome.txt \
 | samtools view -bS -F 4 - \
 | samtools sort -@ ${task.cpus} -o ${file_id}.bam \
-- 
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