Small snippet that generates a genome index and aligns the RNAseq reads.

rnaseq/step3_align/snippet.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+#
+# Align reads against reference genome.
+
+STORAGE="/groups/umcg-griac/tmp01/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 "${OUTPUT}"
+
+# 1) Generate genome index.
+#
+# N.B.:
+# - We're assuming a read size of 100 bp (--sjdbOverhang 100). Refer back to the
+#   previous quality control steps if you are unsure about the size. In case of
+#   reads of varying length, the ideal value is max(ReadLength)-1.
+
+# Where the reference data is stored.
+REFERENCE_DATA="/groups/umcg-griac/prm02/rawdata/reference/genome"
+GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf"
+FASTA_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
+
+STAR \
+    --runThreadN 8 \
+   --runMode genomeGenerate \
+   --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}" "${R2}" \
+    --outSAMtype BAM SortedByCoordinate \
+    --outFileNamePrefix "${ALIGNMENT_OUTPUT}"
+