Add 'rnaseq/step5_count/snippet_counts'

Template structure.
2021-02-12 15:54:26 +01:00 · 2021-02-09 11:20:27 +01:00
9 changed files with 21 additions and 0 deletions
--- a/rnaseq/README.md
+++ b/rnaseq/README.md
@@ -0,0 +1,3 @@
+# RNAseq pipeline
+Snippets for the RNAseq pipeline:
+https://docs.google.com/document/d/1lM1wlz950Q8H6Oi7CWW28FO2tGv5nXYtW0wp8vEUizA
--- a/rnaseq/step1_fastqc/snippet.sh
+++ b/rnaseq/step1_fastqc/snippet.sh
--- a/rnaseq/step2_trim/snippet.sh
+++ b/rnaseq/step2_trim/snippet.sh
--- a/rnaseq/step3_align/snippet.sh
+++ b/rnaseq/step3_align/snippet.sh
--- a/rnaseq/step4_multiqc/snippet.sh
+++ b/rnaseq/step4_multiqc/snippet.sh
--- a/rnaseq/step5_count/snippet.sh
+++ b/rnaseq/step5_count/snippet.sh
--- 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
+
--- a/rnaseq/step6_overall_QC/snippet.R
+++ b/rnaseq/step6_overall_QC/snippet.R
--- a/rnaseq/umi/snippet.pl
+++ b/rnaseq/umi/snippet.pl
Author	SHA1	Message	Date
A.K. Saikumar Jayalatha	96a1e59daf	Add 'rnaseq/step5_count/snippet_counts'	2021-02-12 15:54:26 +01:00
Hylke C. Donker	7ecbc2aee9	Template structure.	2021-02-09 11:20:27 +01:00