JuncBASE protocols

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chevron_left Differential expression Normalization Alternative splicing events identification chevron_right
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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

 (4)
2018
PMCID: 5920379
PMID: 29474581
DOI: 10.1093/jxb/ery062

[…] to be less than 0.05. to filter out false-positive junctions, strict criteria (i.e. an overhang size of more than 20 bp and at least two reads spanning the junctions) were set as cut-off values (). juncbase was used to annotate all as events based on the input genome co-ordinates of all annotated exons and all confidently identified splice junctions (). fisher’s exact tests were used […]

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

[…] 1, −-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 []. 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, […]

2017
PMCID: 5369228
PMID: 28347276
DOI: 10.1186/s12864-017-3656-z

[…] less than 0.05. to filter out false positive junctions, well-studied criteria (i.e., an overhang size of more than 20 bp and at least two reads spanning the junctions) were set as cutoff values []. juncbase was used to annotate all as events based on the input genome coordinates of all annotated exons and all confidently identified splice junctions []. fisher’s exact tests were used to identify […]

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 v0.6 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). […]


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JuncBASE in publications

 (9)
PMCID: 5223305
PMID: 28068922
DOI: 10.1186/s12864-016-3385-8

[…] 1, −-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 []. 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, […]

PMCID: 5357138
PMID: 28177281
DOI: 10.7554/eLife.23268.025

[…] (). we suppressed sf3b1 in sf3b1neutral cells to similar or lower levels as seen at steady state in sf3b1loss cells, and suppressed sf3b1 in sf3b1loss cells to even lower levels ( and ). we used juncbase () and a novel statistical framework to analyze 50,600 splice junctions for intron retention in sf3b1neutral and sf3b1loss cells upon sf3b1 suppression from our rna sequencing data. briefly, […]

PMCID: 4884143
PMID: 27158780
DOI: 10.1038/ng.3564

[…] per million (fpkm) expression estimates as previously described. expression values less than 1 fpkm were set to 1 and all data were log2 transformed. exon skipping of met exon 14 was identified with juncbase as previously described. lists of fusions were obtained from previous studies,3061. fusions for additional tumors were identified with the prada pipeline. for plotting of exonic expression […]

PMCID: 4840452
PMID: 27102525
DOI: 10.1038/srep24964

[…] splicing events was performed without any bias. tophat 2.0.11 was used to predict the splice junctions. splicing analysis was performed for events that had at least 20 total rna-seq reads. juncbase was used to annotate the entire alternative splicing events (cassette exons, alternative 5′ splice site, alternative 3′ splice site, mutually exclusive exons, coordinate cassette exons, […]

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

[…] have allowed for detailed evaluation of whole transcriptomes across many samples. analytical approaches have emerged, including cufflinks and deseq for gene expression analysis and dexseq, miso and juncbase for splicing analysis. however, the use of next-generation sequencing technology for pharmacogenomics research has been limited., although community-wide efforts such as the genotype tissue […]


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

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