RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. It has support for multi-threaded computation, can run on single-end and paired-end data and may produce statistic values in support of it's expression analysis. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. For visualization, user may use RSEM-made bam and wiggle files with UCSC Genome browser or IGV browser from Broad Institute. RSEM can also make transcript read depth plots in pdf format. For this workflow, only limited subset of RSEM toolkit is used. This workflow provides a building block for RNAseq data analysis pipelines.
RSEM 2.0, workflow for accurate quantification of gene and isoform expression from RNA-Seq data
java -jar cromwell.jar run rsem.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
inputBam |
File | Input BAM file with aligned RNAseq reads. |
outputFileNamePrefix |
String | Output prefix, customizable. Default is the input file's basename. |
reference |
String | Name and version of reference genome |
| Parameter | Value | Default | Description |
|---|
| Parameter | Value | Default | Description |
|---|---|---|---|
runRsem.timeout |
Int | 48 | Timeout in hours, needed to override imposed limits |
runRsem.jobMemory |
Int | 12 | Memory in Gb for this job |
| Output | Type | Description |
|---|---|---|
geneResults |
File | expression levels for all genes recorded in the reference |
isoformResults |
File | expression levels for all isoforms recorded in the reference |
transcriptBam |
File | BAM file with additional ZW:f:value, a single precision floating number representing the posterior probability |
This section lists command(s) run by rsem workflow
- Running rsem
rsem workflow runs the following command (excerpt from .wdl file). $RSEM_ROOT pints to rsem's installation directory and defined by the module which a user chooses to use (this is specific to OICR environment).
- INPUT_FILE is a placeholder for an input file.
- RSEM_INDEX_DIR is a placeholder for a direcory with RSEM reference files
- SAMPLE_ID is a placeholder for a sample id
$RSEM_ROOT/bin/rsem-calculate-expression --bam --paired-end INPUT_FILE RSEM_INDEX_DIR SAMPLE_ID
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)
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