Add 'rnaseq/step5_count/snippet_counts'

rnaseq/step3_align/snippet.sh

@@ -1,53 +0,0 @@
-#!/bin/bash
-#
-# Align reads against reference genome.
-
-STORAGE="/groups/umcg-griac/tmp04/rawdata/$(whoami)/step3"
-# Store genome index in this location:.
-GENOME_INDEX="${STORAGE}/genome_index"
-mkdir -p "${GENOME_INDEX}"
-# Store the generated `Aligned.sortedByCoord.out.bam` in this dir.
-ALIGNMENT_OUTPUT="${STORAGE}/alignment"
-mkdir -p "${ALIGNMENT_OUTPUT}"
-
-# 1) Generate genome index.
-#
-# N.B.:
-# - We're assuming a read size of 100 bp (--sjdbOverhang 100). Refer back to the
-#   previous quality control steps if you are unsure about the size. In case of
-#   reads of varying length, the ideal value is max(ReadLength)-1.
-# - We're using gzip compressed reference data (--readFilesCommand zcat), i.e.,
-#   .gtf.gz and fa.gz. If not, you can remove the `zcat` flag.
-
-# Storage location reference data (in this case on calculon).
-REFERENCE_DATA="/groups/umcg-griac/prm02/rawdata/reference/genome"
-GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf.gz"
-FASTA_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
-
-STAR \
-    --runThreadN 8 \
-    --runMode genomeGenerate \
-    --readFilesCommand zcat \
-    --sjdbOverhang 100 \
-    --genomeFastaFiles ${FASTA_FILE} \
-    --sjdbGTFfile ${GTF_FILE} \
-    --genomeDir ${GENOME_INDEX}
-
-
-# 2) Do the actual alignment.
-#
-# N.B.:
-# - We are assuming paired-end, gzip compressed (--readFilesCommand zcat)  FastQ
-#   files.
-
-# THe compressed paired-end FastQ's that we are aligning.
-R1="sample1_R1.fastq.gz"
-R2="sample1_R2.fastq.gz"
-
-STAR \
-    --runThreadN 8 \
-    --readFilesCommand zcat \
-    --readFilesIn "${R1}" "${R2}" \
-    --outSAMtype BAM SortedByCoordinate \
-    --genomeDir ${GENOME_INDEX} \
-    --outFileNamePrefix "${ALIGNMENT_OUTPUT}"

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
+