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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 citations

 (9)
call_split

Thermopriming triggers splicing memory in Arabidopsis

2018
J Exp Bot
PMCID: 5920379
PMID: 29474581
DOI: 10.1093/jxb/ery062
call_split See protocol

[…] d 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 to identify […]

call_split

Herboxidiene triggers splicing repression and abiotic stress responses in plants

2017
BMC Genomics
PMCID: 5369228
PMID: 28347276
DOI: 10.1186/s12864-017-3656-z
call_split See protocol

[…] e 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 […]

call_split

Copy number and gene dependency analysis reveals partial copy loss of wild type SF3B1 as a novel cancer vulnerability

2017
eLife
PMCID: 5357138
PMID: 28177281
DOI: 10.7554/eLife.23268.025
call_split See protocol

[…] . Approximately 50 million reads per sample were generated. FASTQ files were aligned using TOPHAT v1.4 with parameters ‘--mate-inner- dist 300 --mate-std-dev 500 --no-sort-bam --no-convert-bam -p 4’. JuncBase was used to identify read counts at splice junctions (see Appendix Methods). […]

library_books

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

2016
Nat Genet
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 of […]

call_split

Altered microRNA expression and pre mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection

2016
Sci Rep
PMCID: 4840452
PMID: 27102525
DOI: 10.1038/srep24964
call_split See protocol

[…] lternative 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, alter […]

call_split

Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

2016
Pharmacogenomics J
PMCID: 4980276
PMID: 26856248
DOI: 10.1038/tpj.2015.93
call_split See protocol

[…] issue 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). Such […]

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

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