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Commit dfc75475 authored by elabaron's avatar elabaron
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src/RibosomeProfiling.nf : discard reverse alignments in postgenome alignement

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...@@ -472,7 +472,7 @@ hisat2 -x ${index2_id} \ ...@@ -472,7 +472,7 @@ hisat2 -x ${index2_id} \
--trim3 1 \ --trim3 1 \
--trim5 1 \ --trim5 1 \
2> ${file_id}_postgenome.txt \ 2> ${file_id}_postgenome.txt \
| samtools view -bS -F 4 -F 256 - \ | samtools view -bS -F 4 -F 256 -F 16 - \
| samtools sort -@ ${task.cpus} -o ${file_id}_postgenome.bam \ | samtools sort -@ ${task.cpus} -o ${file_id}_postgenome.bam \
&& samtools index ${file_id}_postgenome.bam && samtools index ${file_id}_postgenome.bam
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