SpliceTrap protocols

View SpliceTrap computational protocol

SpliceTrap statistics

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SpliceTrap specifications

Information


Unique identifier OMICS_01292
Name SpliceTrap
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output format TXT, RAW, NUMS, LOG
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Version 0.90.5
Stability Stable
Requirements
Qsub, bowtie, RMAP
Maintained Yes

Versioning


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Maintainers


  • person_outline Michael Zhang <>
  • person_outline Jie Wu <>

Additional information


http://rulai.cshl.edu/splicetrap/doc/index.html

Publication for SpliceTrap

SpliceTrap in pipelines

 (2)
2017
PMCID: 5662751
PMID: 29084942
DOI: 10.1038/s41467-017-01126-x

[…] of rna-seq data was performed with the deseq package available from bioconductor (http://www.bioconductor.org). to identify differential splicing events between samples, we used the software splicetrap (supplementary data ). to assess whether sfpq interferes with alternative polyadenylation sites and the length of the 3′utrs we used the software dapars. our analyses did not find […]

2014
PMCID: 3896118
PMID: 24448406
DOI: 10.7554/eLife.01201.014

[…] at p1, emxko and wild-type samples generated 354m and 317m mapped reads respectively. alternative exon inclusion levels were determined by additional mapping to an exon duo and trio database using splicetrap (). gene ontology analysis was performed using david ()., mouse primary cortical cultures were prepared from e15-16 embryos and primary hippocampal cultures from e18 embryos as described […]


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SpliceTrap in publications

 (15)
PMCID: 5697891
PMID: 29121637
DOI: 10.1371/journal.pgen.1007033

[…] usage., the database of as events that we used to compare splice site usage was generated using a combination of two methods. first, we generated an exon isoform database for c. elegans using splicetrap v.0.90.1 [] and transcript annotations from ensembl. splicetrap generates this database by subdividing each transcript isoform into exon trios to query for alternative splicing […]

PMCID: 5662751
PMID: 29084942
DOI: 10.1038/s41467-017-01126-x

[…] of rna-seq data was performed with the deseq package available from bioconductor (http://www.bioconductor.org). to identify differential splicing events between samples, we used the software splicetrap (supplementary data ). to assess whether sfpq interferes with alternative polyadenylation sites and the length of the 3′utrs we used the software dapars. our analyses did not find […]

PMCID: 5513350
PMID: 28716093
DOI: 10.1186/s12915-017-0398-y

[…] ws220 version of wormbase were classified into different types of alternative splicing events using two different methodologies, namely dedb (http://proline.bic.nus.edu.sg/dedb/methodology.html) and splicetrap (http://rulai.cshl.edu/splicetrap/). information on the classes of alternative splicing events and the classification process are available on the websites corresponding to the methods. […]

PMCID: 5249219
PMID: 28107452
DOI: 10.1371/journal.pone.0170576

[…] mice to generate lines, positive studs were identified and mated with c57bl/6 wildtype females and embryos were collected for analysis., the bay genomics es cell line rrf373 containing the β-geo splicetrap vector, pgt0lxf [] was obtained from the mutant mouse regional resource centers (mmrrc, davis, usa) (www.mmrrc.org/). the e14 mutant es cell line (g418-resistant; 129p2/ola) was used […]

PMCID: 5423405
PMID: 28024152
DOI: 10.1038/ni.3654

[…] and intron sequences were retrieved using r/bioconductor’s (http://www.bioconductor.org) bsgenome packages. all exons and flanking introns (with explicit start-end coordinates) defined in txdb (for splicetrap) and ensmart65 (for altanalyze) were used as search spaces to compute the total occurrence and location of each predicted binding site (see below). entire exon blocks (merged ensembl […]


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SpliceTrap institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA; Bioinformatics Div., Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, China
SpliceTrap funding source(s)
Supported by National Institutes of Health (GM74688).

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