Gohr, AndréIrimia Martínez, Manuel2019-04-262019-04-262019Gohr A, Irimia M. Matt: Unix tools for alternative splicing analysis. Bioinformatics. 2019;35(1):130-2. DOI 10.1093/bioinformatics/bty6061367-4803http://hdl.handle.net/10230/37138Summary: 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.application/pdfeng© 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/35/1/130/5053311info:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/bioinformatics/bty606info:eu-repo/semantics/openAccess