BitSeq protocols

BitSeq specifications

Information


Unique identifier OMICS_01269
Name BitSeq
Alternative name Bayesian inference of transcripts from sequencing data
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, R
Computer skills Advanced
Version 0.7.5
Stability Stable
Requirements GNU make, g++, zlib
Maintained Yes

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Maintainer


  • person_outline Magnus Rattray <>

Publication for Bayesian inference of transcripts from sequencing data

BitSeq IN pipelines

 (5)
2017
PMCID: 5334791
PMID: 28099430
DOI: 10.1038/nmeth.4177

[…] -p 6 -a -m 100 -minins 0 -maxins 5000 -fr -sam -chunkmbs 200. duplicate reads were removed with picard’s markduplicates utility using standard parameters, followed by transcript quantification with bitseq22 using the markov chain monte carlo method and standard parameters. to obtain gene-level quantifications, we assigned to each gene the expression value of its most highly expressed […]

2016
PMCID: 5069555
PMID: 27647875
DOI: 10.15252/embj.201694857

[…] (cunningham et al, 2015) using the segemehl software (hoffmann et al, 2009). the estimation of the transcript expression as well as the differential expression (de) analysis was done using the bitseq software package (glaus et al, 2012)., total rna was resolved on 10% denaturing polyacrylamide gel and transferred to hybond‐n+ membrane (ge healthcare) by electroblotting (bio‐rad). […]

2015
PMCID: 4511015
PMID: 26201343
DOI: 10.1186/s13059-015-0702-5

[…] of the fragment/read length distribution, we calculated these from the alignment files with a custom script. in the following, the steps taken to execute each surveyed program are outlined., bitseq [67, 68] uses as input transcript sequences in fasta format and alignments of reads to the transcriptome in sam or bam format, sorted by read name (randomized). we have used the command-line […]

2015
PMCID: 4511015
PMID: 26201343
DOI: 10.1186/s13059-015-0702-5

[…] 68] uses as input transcript sequences in fasta format and alignments of reads to the transcriptome in sam or bam format, sorted by read name (randomized). we have used the command-line version of bitseq (version 0.7.5), but an r/bioconductor version is also available., the first step in bitseq is to parse the alignment file to calculate probabilities of individual reads originating […]

2015
PMCID: 4511015
PMID: 26201343
DOI: 10.1186/s13059-015-0702-5

[…] in sam or bam format, sorted by read name (randomized). we have used the command-line version of bitseq (version 0.7.5), but an r/bioconductor version is also available., the first step in bitseq is to parse the alignment file to calculate probabilities of individual reads originating from individual transcripts:parsealignment \ <alignments_transcriptome> --trseqfile […]

BitSeq institution(s)
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

BitSeq review

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Andrew Miller

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Desktop
A great tool for RNA-seq analyses !