Updated htseq-count with extra comments.

rnaseq/step5_count/snippet.sh

@@ -13,9 +13,15 @@ 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.
+# - If you are processing multiple files, consider using the `--nprocesses` flag
+#   to distribute computation of the files to different cores.
+# - The BAM file must be position sorted. If you used STAR with the
+#   `SortedByCoordinate` option you should be okay. If not, sort your BAM file
+#   using `samtools sort`.
+# - By default, strand aware library preparation is assumed. If not, specify the
+#   `--stranded` flag.
 htseq-count \
+    --order pos \
     ${BAM} \
     ${GTF_FILE} \
     > ${COUNT_OUTPUT}/counts.txt