Added htseq-count snippet + updated STAR snippet indicating prebuilt genome index.

rnaseq/step5_count/snippet.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
+COUNT_OUTPUT="${PROJECT_DIRECTORY}/step5"
+mkdir -p "${COUNT_OUTPUT}"
+
+# Storage location of annotation on Gearshift.
+REFERENCE_DATA="/groups/umcg-griac/prm03/rawdata/reference/genome"
+GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf"
+
+# Where our alignment file was stored.
+BAM="${PROJECT_DIRECTORY}/step3/alignment/sample1_Aligned.sortedByCoord.out.bam"
+
+# Compute counts using htseq-count.
+#
+# N.B.:
+# - If you are processing multiple files, you can use the --nprocesses flag to
+#   compute the files in parallel.
+htseq-count \
+    ${BAM} \
+    ${GTF_FILE} \
+    > ${COUNT_OUTPUT}/counts.txt