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06. Generate genome indexes
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06. Generate genome indexes
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#!/bin/bash
#SBATCH -n 8 # use all 32 cores on the SMP node
##SBATCH -p private
##SBATCH --mem-per-cpu=16000
#SBATCH --job-name=GRCh38Reference_Y_excluded_VP64
#SBATCH -t 0-4:0 # time
#SBATCH -A mwilsons
#SBATCH -o slurm.GRCh38Reference_Y_excluded_VP64.out
#SBATCH -e slurm.GRCh38Reference_Y_excluded_VP64.err
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected] # If you want it to email you when the job is completed or fails
################################
#--------------------------
# 1. start timer
#--------------------------
date
#--------------------------
# 2. move to the appropriate directory
#--------------------------
cd /home/kcolney/cancer_HaynesLab/GRCh38_Y_excluded_VP64
#--------------------------
# 3. load module
#--------------------------
module load star/2.4.2a
module load java/latest
module load samtools/1.3.1
#--------------------------
# 4. Reference genome for STAR format
#--------------------------
STAR --genomeDir /home/kcolney/cancer_HaynesLab/GRCh38_Y_excluded_VP64 --runMode genomeGenerate --genomeFastaFiles /home/kcolney/cancer_HaynesLab/GRCh38_Y_excluded_VP64/GRCh38.p7_Y_excluded_VP64.fa --sjdbGTFfile gencode.v25.chr_patch_hapl_scaff.annotation.gtf --runThreadN 12
#--------------------------
# 5. create reference dictionary
#--------------------------
java -Xmx14g -jar /home/kcolney/ngcchome/tools2/picard.jar CreateSequenceDictionary R=GRCh38.p7_Y_excluded_VP64.fa O=GRCh38.p7_Y_excluded_VP64.fa.dict
#--------------------------
# 6. create .fai reference
#--------------------------
samtools faidx GRCh38.p7_Y_excluded_VP64.fa
#--------------------------
# 7. end timer
#--------------------------
date