RSEM specifications

Unique identifier:
OMICS_01287
Alternative name:
rsem
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
1.3.0
Requirements:
Bowtie
Name:
RNA-Seq by Expectation-Maximization
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++, Perl, Python, R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

versioning

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No versioning.

RSEM distribution

download

RSEM support

Documentation

Maintainer

  • Colin Dewey <>

Additional information

https://github.com/bli25ucb/RSEM_tutorial

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Credits

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Publications

Institution(s)

Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA

Funding source(s)

Supported in part by Dr. James Thomson’s MacArthur Professorship and by Morgridge Institute for Research support for Computation and Informatics in Biology and Medicine, and by NIH grant 1R01HG005232-01A1.

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Fabien Pichon

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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...

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