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.
Operation: Gene expression analysis;RNA-Seq quantification
Software interface: Command-line user interface
License: GNU General Public License v3
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
Contact: Bo Li email@example.com | Colin N Dewey firstname.lastname@example.org
- 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
- PMID: 21816040
- PMC: PMC3163565
Download and documentation
Home page: http://deweylab.github.io/RSEM/
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