Journal
BIOINFORMATICS
Volume 35, Issue 1, Pages 130-132Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty606
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Funding
- European Research Council [ERC-StG-LS2-637591, ERC-AdG-MASCP-670146]
- Spanish Ministry of Economy and Competitiveness [BFU2014-55076-P, BFU2014-55058-P]
- EMBL
- CRG, Centro de Excelencia Severo Ochoa [SEV-2012-0208]
- CERCA programme
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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.
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