Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

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  • dc.contributor.author Althammer, Sonja Danielaca
  • dc.contributor.author González-Vallinas Rostes, Juan, 1983-ca
  • dc.contributor.author Ballaré, Cecilia Juliaca
  • dc.contributor.author Beato, Miguelca
  • dc.contributor.author Eyras Jiménez, Eduardoca
  • dc.date.accessioned 2015-12-15T17:46:55Z
  • dc.date.available 2015-12-15T17:46:55Z
  • dc.date.issued 2011
  • dc.description.abstract MOTIVATION: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. RESULTS: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. AVAILABILITY: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxyca
  • dc.description.sponsorship Generalitat de Catalunya by FI grant (to S.A.); Spanish Ministry of Science (MICINN) by FPI grant (to J.G.V.); MICINN grant BIO2008-01091 (to E.E.); European Commission grant EURASNET-(LSHG-CT-2005-518238) (to E.E.).
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics. 2011;27(24):3333-40. DOI: 10.1093/bioinformatics/btr570ca
  • dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btr570
  • dc.identifier.issn 1367-4803
  • dc.identifier.uri http://hdl.handle.net/10230/25438
  • dc.language.iso engca
  • dc.publisher Oxford University Pressca
  • dc.relation.ispartof Bioinformatics. 2011;27(24):3333-40
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/518238
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2008-01091
  • dc.rights © 2011 Althammer et al. This is an Open Access article distributed under the terms of a Creative Commons Attribution Licenseca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.subject.other Cromatinaca
  • dc.subject.other Regulació genèticaca
  • dc.subject.other Biologia computacionalca
  • dc.title Pyicos: a versatile toolkit for the analysis of high-throughput sequencing dataca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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