Dataset Information
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
Ontology highlight
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/galaxyContact
eduardo.eyras@upf.eduSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Althammer S
PROVIDER: S-EPMC3232367 | biostudies-literature | 2011 Dec
REPOSITORIES: biostudies-literature
Publications
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
Bioinformatics (Oxford, England) 20111012 24
<h4>Motivation</h4>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.<h4>Results</h4>We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punct ...[more]
