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