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Use BAM files for htseq-count.

master
Hylke C. Donker 1 year ago
parent
commit
35f356dd33
  1. 3
      rnaseq/step5_count/snippet.sh

3
rnaseq/step5_count/snippet.sh

@ -22,6 +22,7 @@ BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam" @@ -22,6 +22,7 @@ BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam"
# `--stranded` flag.
htseq-count \
--order pos \
-f bam \
${BAM} \
${GTF_FILE} \
> ${COUNT_OUTPUT}/counts.txt
> ${COUNT_OUTPUT}/counts.txt

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