161212 Generating a genome index - npslindstrom/DE-analysis GitHub Wiki
So over the weekend I resubmitted the sbatch script for unzipping the reference genome and it seems to have worked out. Thus the next step was to use the reference genome to make an indexed reference genome. I used the GTF-files of new genome annotations from Gencode: http://www.gencodegenes.org/releases/current.html
Hopefully it works.
The sbatch script was written like this:
#!/bin/bash
# OPTIONS:
#SBATCH -A g2016025
#SBATCH -t 2:00:00
#SBATCH -o ../logs/star.aln.out
#SBATCH -e ../logs/star.aln.err
#SBATCH -p node -n 8
#SBATCH --mail-type=All
#SBATCH [email protected]
module load bioinfo-tools
module load star/2.5.0a
cd /home/nilsl/lncRNA_proj
star
--runThreadN 8
--runMode genomeGenerate
--genomeDir ../genomedir
--genomeFastaFiles ../Homo_sapiens.GRCh38.dna.primary_assembly.fa
--sjdbGTFfile ../annotationGTF/gencode.v25.annotation.gtf
--sjdbOverhang 100