step1.qsub

#!/bin/bash
source /etc/profile
#$ -S /bin/bash
#$ -pe pvm 16
module load /mnt/storage/spack/share/spack/modules/linux-ubuntu16.04-x86_64/star-2.7.2b-gcc-5.4.0-fqvrpgi
module load /mnt/storage/spack/share/spack/modules/linux-ubuntu16.04-x86_64/rsem-1.3.1-gcc-5.4.0-ml3p6ok

wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/GRCh38.primary_assembly.genome.fa.gz
gunzip GRCh38.primary_assembly.genome.fa.gz
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.annotation.gtf.gz
gunzip gencode.v38.annotation.gtf.gz

rsem-prepare-reference --gtf gencode.v38.annotation.gtf --star GRCh38.primary_assembly.genome.fa gencode_v38

#Replace RNAseqfastq with your RNA-seq fastq file and NAME with the output file prefix
rsem-calculate-expression --paired-end --strandedness none --append-names --star RNAseqfastq_1.fq RNAseqfastq_2.fq gencode_v38 NAME