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Updated htseq-count with extra comments.

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This commit is contained in:
Hylke C. Donker 2021-02-25 16:59:57 +01:00
parent e852072235
commit 1c42a61e48
1 changed files with 8 additions and 2 deletions
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10
rnaseq/step5_count/snippet.sh
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@ -13,9 +13,15 @@ BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam"
# Compute counts using htseq-count. # Compute counts using htseq-count.
# #
# N.B.: # N.B.:
# - If you are processing multiple files, you can use the --nprocesses flag to # - If you are processing multiple files, consider using the `--nprocesses` flag
# compute the files in parallel. # 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 \ htseq-count \
--order pos \
${BAM} \ ${BAM} \
${GTF_FILE} \ ${GTF_FILE} \
> ${COUNT_OUTPUT}/counts.txt > ${COUNT_OUTPUT}/counts.txt