RSEM

RSEM (RNA-Seq by Expectation-Maximization) is a tool for the quantification of RNA-seq data. The RSEM algorithm uses the expectation-maximization technique, it can operate with and without a reference, and reports transcripts per million mapped reads (TPM). RSEM scales linearly with the amount of alignment quantity and uses The Bowtie tool for the read alignments.

Topic

RNA-seq;Gene expression;Transcriptomics

Detail

  • Operation: Gene expression analysis;RNA-Seq quantification

  • Software interface: Command-line user interface

  • Language: C++;Perl

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.3.1

  • Credit: Dr. James Thomson's MacArthur Professorship, Morgridge Institute for Research support for Computation and Informatics in Biology and Medicine, the National Institutes of Health (NIH).

  • Input: FASTA, FASTQ

  • Output: -

  • Contact: Bo Li bli25@berkeley.edu | Colin N Dewey cdewey@biostat.wisc.edu

  • Collection: -

  • Maturity: -

Publications

  • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
  • Li B and Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. 2011; 12:323. doi: 10.1186/1471-2105-12-323
  • https://doi.org/10.1186/1471-2105-12-323
  • PMID: 21816040
  • PMC: PMC3163565

Download and documentation

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