URL: http://www.lgm.upmc.fr/parseq/
Proper Citation: Parseq (RRID:SCR_003464)
Description: Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.
Abbreviations: Parseq
Resource Type: software resource
Defining Citation: PMID:24470570
Keywords: rna-seq, genome, transcription, bio.tools
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