This post is to show how to make STAR and kallisto index for rice MSU7 annotations.
1. Download genome files.
# genome sequence
wget http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.con
# gff3 annotation
wget http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.gff3
# cdna sequences
wget http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.cdna
2. Convert GFFF3 to GTF
module load cufflinks/2.2.1
gffread all.gff3 -T -o all.gtf
3. Make kallisto index
module load kallisto/intel/0.43.0
kallisto index -i osj_msu7_kallisto.idx all.cdna
4. Build STAR index.
I submitted a slurm job, STAR_genome_index_rice.slurm showing below.
#!/bin/bash
#SBATCH --output=/scratch/cgsb/coruzzi/jh6577/GenomeFile/rice_MSU7/STAR_index/STAR_genome_build_%A_%a.out
#SBATCH --error=/scratch/cgsb/coruzzi/jh6577/GenomeFile/rice_MSU7/STAR_index/STAR_genome_build_%A_%a.err
#SBATCH -J STAR_genome_build
#SBATCH --cpus-per-task=12
#SBATCH --mem=40GB
#SBATCH --mail-type=END
##SBATCH --mail-user=jh6577@nyu.edu
module purge
module load star/intel/2.5.3a
STAR --runMode genomeGenerate --runThreadN 12 --genomeDir //scratch/cgsb/coruzzi/jh6577/GenomeFile/rice_MSU7/STAR_index/ --genomeFastaFiles /scratch/cgsb/coruzzi/jh6577/GenomeFile/rice_MSU7/all.con --sjdbGTFfile /scratch/cgsb/coruzzi/jh6577/GenomeFile/rice_MSU7/all.gtf