From 1c42a61e48815a611ca303c19e9bd54d1fac98d2 Mon Sep 17 00:00:00 2001 From: "Hylke C. Donker" Date: Thu, 25 Feb 2021 16:59:57 +0100 Subject: [PATCH] Updated htseq-count with extra comments. --- rnaseq/step5_count/snippet.sh | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/rnaseq/step5_count/snippet.sh b/rnaseq/step5_count/snippet.sh index ec910ee..6aff43a 100644 --- a/rnaseq/step5_count/snippet.sh +++ b/rnaseq/step5_count/snippet.sh @@ -13,9 +13,15 @@ BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam" # Compute counts using htseq-count. # # N.B.: -# - If you are processing multiple files, you can use the --nprocesses flag to -# compute the files in parallel. +# - If you are processing multiple files, consider using the `--nprocesses` flag +# to distribute computation of the files to different cores. +# - The BAM file must be position sorted. If you used STAR with the +# `SortedByCoordinate` option you should be okay. If not, sort your BAM file +# using `samtools sort`. +# - By default, strand aware library preparation is assumed. If not, specify the +# `--stranded` flag. htseq-count \ + --order pos \ ${BAM} \ ${GTF_FILE} \ > ${COUNT_OUTPUT}/counts.txt \ No newline at end of file