From 35f356dd3336f2bd8614136498982fc966114189 Mon Sep 17 00:00:00 2001
From: "Hylke C. Donker" <hylke.donker@gmail.com>
Date: Wed, 17 Mar 2021 17:06:02 +0100
Subject: [PATCH] Use BAM files for htseq-count.

---
 rnaseq/step5_count/snippet.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/rnaseq/step5_count/snippet.sh b/rnaseq/step5_count/snippet.sh
index 6aff43a..fd3270c 100644
--- 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
\ No newline at end of file
+    > ${COUNT_OUTPUT}/counts.txt