Matt: Unix tools for alternative splicing analysis

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• dc.contributor.author Gohr, André
• dc.contributor.author Irimia Martínez, Manuel
• dc.date.accessioned 2019-04-26T07:35:51Z
• dc.date.available 2019-04-26T07:35:51Z
• dc.date.issued 2019
• dc.description.abstract Summary: Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality. Availability and implementation: matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules/the R Base package simplifying its installation.
• dc.description.sponsorship This work was supported by the European Research Council [ERC-StG-LS2-637591 and ERC-AdG-MASCP-670146], the Spanish Ministry of Economy and Competitiveness [BFU2014-55076-P and BFU2014-55058-P], the EMBL partnership, and the CRG (SEV-2012-0208), Centro de Excelencia Severo Ochoa and CERCA programme.
• dc.format.mimetype application/pdf
• dc.identifier.citation Gohr A, Irimia M. Matt: Unix tools for alternative splicing analysis. Bioinformatics. 2019;35(1):130-2. DOI 10.1093/bioinformatics/bty606
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/bty606
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/37138
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2019;35(1):130-2
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55076-P
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55058-P
• dc.rights © Oxford University Press. This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Gohr A, Irimia M. Matt: Unix tools for alternative splicing analysis. Bioinformatics. 2019; 35(1):130-132. DOI 10.1093/bioinformatics/bty606 is available online at: https://academic.oup.com/bioinformatics/article/35/1/130/5053311
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.title Matt: Unix tools for alternative splicing analysis
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/acceptedVersion