Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
Bioinformatics
; 27(24): 3333-40, 2011 Dec 15.
Article
em En
| MEDLINE
| ID: mdl-21994224
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 eduardo.eyras@upf.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Espanha