rSeq: RNA-Seq Analyzer

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Updates (These are the major updates only. For all updates, see HISTORY.txt)

February 9, 2015 - rSeq 0.2.1 now also supports the whole genome in a single fasta file when generating transcripts

March 3, 2014 - rSeq 0.2.0 now supports annotation files in GTF format, refFlat format and ucscKnownGene format.

July 22, 2012 - rSeq 0.1.0 now supports aligners which output in the SAM format. We have tested with BWA, Bowtie and Bowtie2. Note: since rSeq 0.1.0 a new way for generating transcripts and estimating gene and isoform expression values is used. The old way (here are the old user manual and old FAQ) still works but not recommended.

March 25, 2010 - rSeq 0.0.5 now supports isoform-specific gene expression estimation and paired-end RNA-Seq.

September 12, 2009 - RSAT is renamed as rSeq.

February 9, 2009 - RSAT 0.0.1 is online.


rSeq is a set of tools for RNA-Seq data analysis. It consists of programs that deal with many aspects of RNA-Seq data analysis, such as read quality assessment, reference sequence generation, sequence mapping, gene and isoform expressions (RPKMs) estimation, etc. There are also many other features that will be gradually added into rSeq in the future.

For questions, please read the FAQ first.


rSeq was started in the Wong Lab and is developed and maintained by Hui Jiang.


Jiang, H., Wong, W.H. (2009) Statistical Inferences for Isoform Expression in RNA-Seq, Bioinformatics, 25(8), 1026–1032. [online]

Salzman, J., Jiang, H., Wong, W. H. (2011) Statistical Modeling of RNA-Seq Data, Statistical Science, 26 (1): 62-83. [online][arxiv]


Anyone can use the source codes, documents or the excutable file of rSeq free of charge for non-commercial use. For commercial use, please contact the author.


0.2.2 source (for all platform)