Add 'rnaseq/step5_count/snippet_counts'

2021-02-12 15:54:26 +01:00
1 changed files with 18 additions and 0 deletions
--- a/rnaseq/step5_count/snippet_counts
+++ b/rnaseq/step5_count/snippet_counts
@ -0,0 +1,18 @@
+## Generate Raw Counts using FeatureCounts/HTSeqCounts 
+
+## Load package Subread (packge within which FeatureCounts is present)
+
+ ml Subread/1.6.4-foss-2015b FeatureCounts
+
+## Features used in FeatureCounts : 
+## -s : reversely stranded 
+## -T : number of threads used 
+## -a : reference genome 
+## -o : output file 
+
+ featureCounts \
+ --a "path to reference genome" \
+ --T 6 \
+ --o "path to output file" \
+ --s 2
+