Rsem

Introduction

Rsem is a software package for estimating gene and isoform expression levels from RNA-Seq data.

For more information, please check:
Dockerhub: https://hub.docker.com/r/zhan4429/rsem
Home page: https://github.com/deweylab/RSEM

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.3.3

BELL

1.3.3

GAUTSCHI

1.3.3

NEGISHI

1.3.3

SCHOLAR

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-for-ebseq-calculate-clustering-info

  • rsem-for-ebseq-find-DE

  • rsem-for-ebseq-generate-ngvector-from-clustering-info

  • rsem-gen-transcript-plots

  • rsem-generate-data-matrix

  • 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-sam-validator

  • rsem-scan-for-paired-end-reads

  • rsem-simulate-reads

  • rsem-synthesis-reference-transcripts

  • rsem-tbam2gbam

Module

You can load the modules by:

module load biocontainers
module load rsem

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 clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers rsem

# Your rsem workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers rsem

# Your rsem workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers rsem

# Your rsem workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers rsem

# Your rsem workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers rsem

# Your rsem workflow...