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