JuncBASE protocols

JuncBASE specifications

Information


Unique identifier OMICS_01335
Name JuncBASE
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.6
Stability Stable
Maintained Yes

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Publication for JuncBASE

JuncBASE IN pipelines

 (3)
2017
PMCID: 5223305
PMID: 28068922
DOI: 10.1186/s12864-016-3385-8

[…] −-max-intron-length 17325, and --min-intron-length 81). a total of 15 million reads were randomly selected from each sample for analysis to make sure that the comparison was at the same level [14]. juncbase was used to annotate all as events (cassette exons, alternative 5′ splice site, alternative 3′ splice site, mutually exclusive exons, coordinate cassette exons, alternative first exons, […]

2016
PMCID: 4980276
PMID: 26856248
DOI: 10.1038/tpj.2015.93

[…] type. throughout, gene estimates are used unless isoforms are specifically mentioned., to discover novel splice events and analyze differential splicing, the subsampled reads were run through the juncbase v0.610 pipeline. juncbase uses junction reads from an rna-seq experiment to calculate inclusion and exclusion of individual splicing events. these are measured as percent spliced in (psi). […]

2016
PMCID: 4980276
PMID: 26856248
DOI: 10.1038/tpj.2015.93

[…] estimates are used unless isoforms are specifically mentioned., to discover novel splice events and analyze differential splicing, the subsampled reads were run through the juncbase v0.610 pipeline. juncbase uses junction reads from an rna-seq experiment to calculate inclusion and exclusion of individual splicing events. these are measured as percent spliced in (psi). such measures are generally […]

JuncBASE institution(s)
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA

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