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BitSeq |Approximate inference of transcript expression from RNA-seq data


An application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

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1 user review

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Andrew Miller

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A great tool for RNA-seq analyses !

BitSeq forum

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BitSeq classification

BitSeq specifications

Unique identifier:
Software type:
Restrictions to use:
Programming languages:
C++, R
Bayesian inference of transcripts from sequencing data
Command line interface
Operating system:
Computer skills:
GNU make, g++, zlib

BitSeq distribution


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BitSeq support



  • Magnus Rattray <>


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School of Computer Science, University of Manchester, Oxford Road, Manchester, UK; Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, University of Helsinki, Finland; Department of Computer Science and Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK

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