Use BAM files for htseq-count.

2021-03-17 17:06:02 +01:00 · 2021-03-17 17:06:02 +01:00 · 35f356dd33
commit 35f356dd33
parent 4b449ded08
1 changed files with 2 additions and 1 deletions
--- a/rnaseq/step5_count/snippet.sh
+++ b/rnaseq/step5_count/snippet.sh
@ -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