RSEM

Introduction

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. Further information can be found here: https://deweylab.github.io/RSEM/.

Versions

  • 1.3.3

Commands

  • rsem-bam2readdepth

  • rsem-bam2wig

  • rsem-build-read-index

  • rsem-calculate-credibility-intervals

  • rsem-calculate-expression

  • rsem-control-fdr

  • rsem-extract-reference-transcripts

  • rsem-generate-data-matrix

  • rsem-generate-ngvector

  • rsem-gen-transcript-plots

  • rsem-get-unique

  • rsem-gff3-to-gtf

  • rsem-parse-alignments

  • rsem-plot-model

  • rsem-plot-transcript-wiggles

  • rsem-prepare-reference

  • rsem-preref

  • rsem-refseq-extract-primary-assembly

  • rsem-run-ebseq

  • rsem-run-em

  • rsem-run-gibbs

  • rsem-run-prsem-testing-procedure

  • rsem-sam-validator

  • rsem-scan-for-paired-end-reads

  • rsem-simulate-reads

  • rsem-synthesis-reference-transcripts

  • rsem-tbam2gbam

Dependencies

STAR v2.7.9a, Bowtie v1.2.3, Bowtie2 v2.3.5.1, HISAT2 v2.2.1 were included in the container image. So users do not need to provide the dependency path in the RSEM parameter.

Module

You can load the modules by:

module load biocontainers
module load rsem/1.3.3

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run RSEM on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=rsem
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers rsem/1.3.3

rsem-prepare-reference --gtf Homo_sapiens.GRCh38.105.gtf --bowtie Homo_sapiens.GRCh38.dna.primary_assembly.fa Gh38_bowtie  -p 24
rsem-prepare-reference --gtf Homo_sapiens.GRCh38.105.gtf --bowtie2 Homo_sapiens.GRCh38.dna.primary_assembly.fa Gh38_bowtie2  -p 24
rsem-prepare-reference --gtf Homo_sapiens.GRCh38.105.gtf --hisat2-hca  Homo_sapiens.GRCh38.dna.primary_assembly.fa Gh38_hisat2  -p 24
rsem-prepare-reference --gtf Homo_sapiens.GRCh38.105.gtf --star Homo_sapiens.GRCh38.dna.primary_assembly.fa Gh38_star  -p 24
rsem-calculate-expression --paired-end --star -p 24 SRR12095148_1.fastq SRR12095148_2.fastq  Gh38_star SRR12095148_rsem_expression