RSEM¶
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
RSEM is available as a module on Apocrita.
Usage¶
To run the default version of RSEM, simply load the
rsem module:
$ module load rsem
Usage: <command> [options] [--help]
The following commands are available:
convert-sam-for-rsem rsem-plot-model
extract-transcript-to-gene-map-from-trinity rsem-plot-transcript-wiggles
rsem-bam2readdepth rsem-prepare-reference
rsem-bam2wig rsem-preref
rsem-build-read-index rsem-refseq-extract-primary-assembly
rsem-calculate-credibility-intervals rsem-run-em
rsem-calculate-expression rsem-run-gibbs
rsem-extract-reference-transcripts rsem-sam-validator
rsem-generate-data-matrix rsem-scan-for-paired-end-reads
rsem-gen-transcript-plots rsem-simulate-reads
rsem-get-unique rsem-synthesis-reference-transcripts
rsem-gff3-to-gtf rsem-tbam2gbam
rsem-parse-alignments
Usage for each command can be shown by using the command with the --help
option. For more detailed documentation please check the link to the Github
page listed below.
Core Usage
Not all RSEM commands support multi-threading; Commands which do support
multi-threading should include a -p ${NSLOTS} or
--num-threads ${NSLOTS} switch to use the correct number of cores.
Please check the documentation before running jobs.
Example job¶
Serial job¶
Here is an example job running on 2 cores and 4GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load rsem
# Convert a transcript coordinate BAM alignments file into a genomic coordinate
BAM alignments file
rsem-tbam2gbam reference_name unsorted_transcript_bam_input genome_bam_output -p {NSLOTS}