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Use BAM files for htseq-count.

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This commit is contained in:
Hylke C. Donker 2021-03-17 17:06:02 +01:00
parent 4b449ded08
commit 35f356dd33
1 changed files with 2 additions and 1 deletions
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3
rnaseq/step5_count/snippet.sh
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@ -22,6 +22,7 @@ BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam"
# `--stranded` flag. # `--stranded` flag.
htseq-count \ htseq-count \
--order pos \ --order pos \
-f bam \
${BAM} \ ${BAM} \
${GTF_FILE} \ ${GTF_FILE} \
> ${COUNT_OUTPUT}/counts.txt > ${COUNT_OUTPUT}/counts.txt