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Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data.
Bioinformatics. 2011 Oct 12;
Authors: Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E
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/galaxy CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplemental data are available at Bioinformatics online.
PMID: 21994224 [PubMed - as supplied by publisher]
More...
Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data.
Bioinformatics. 2011 Oct 12;
Authors: Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E
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/galaxy CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplemental data are available at Bioinformatics online.
PMID: 21994224 [PubMed - as supplied by publisher]
More...