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 \ -- GitLab