Applications/Rsem

Application Details

• Description: RSEM can extract reference transcripts from a genome if you provide it with gene annotations in a GTF/GFF3 file
• Version:1.3.0
• Modules: rsem/1.3.0
• Licence: GNU General Public License v3.

Usage

Prior-enhanced RSEM (pRSEM) uses complementary information (e.g. ChIP-seq data) to allocate RNA-seq multi-mapping fragments. We included pRSEM code in the subfolder pRSEM/ as well as in RSEM’s scripts rsem-prepare-reference and rsem-calculate-expression.

Simulation

RSEM provides users the rsem-simulate-reads program to simulate RNA-Seq data based on parameters learned from real data sets. Run

rsem-simulate-reads

to get usage information or read the following subsections.

rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]

Example

Suppose we want to simulate 50 millon single-end reads with quality scores and use the parameters learned from Example. In addition, we set theta0 as 0.2 and output_name as simulated_reads. The command is:

[username@login]$ module add rsem/1.3.0
[username@login]$ rsem-simulate-reads /ref/mouse_0 mmliver_single_quals.stat/mmliver_single_quals.model mmliver_single_quals.isoforms.results 0.2 50000000 simulated_reads 

Further Information

• https://deweylab.github.io/RSEM/

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