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RNA-Seq by Expectation-Maximization RSEM

An user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data.

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1 user review

1 user review

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

Usefull if you want to estimate isoform expression in your RNA-seq. It uses Bowtie by default but you can map with another mapper and just use BAM/SAM file, so RSEM is quite flexible. Routinely used in TCGA workflow, but I would like to highlight that their RSEM UCSC isoforms IDs are sometimes different from Official UCSC isoforms IDs, no idea why...

RSEM forum

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RSEM versioning

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No versioning.

RSEM classification

RSEM specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Conda:
https://bioconda.github.io/recipes/rsem/README.html
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable
Debian:
https://packages.qa.debian.org/r/rsem.html

Credits

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Publications

Institution(s)

Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA

Link to literature

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