NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling.
Bioinformatics
; 37(5): 596-602, 2021 05 05.
Article
em En
| MEDLINE
| ID: mdl-32991679
ABSTRACT
MOTIVATION The discovery of sequence motifs mediating DNA-protein binding usually implies the determination of binding sites using high-throughput sequencing and peak calling. The determination of peaks, however, depends strongly on data quality and is susceptible to noise. RESULTS:
Here, we present a novel approach to reliably identify transcription factor-binding motifs from ChIP-Seq data without peak detection. By evaluating the distributions of sequencing reads around the different k-mers in the genome, we are able to identify binding motifs in ChIP-Seq data that yield no results in traditional pipelines. AVAILABILITY AND IMPLEMENTATION NoPeak is published under the GNU General Public License and available as a standalone console-based Java application at https//github.com/menzel/nopeak. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Sequenciamento de Nucleotídeos em Larga Escala
/
Sequenciamento de Cromatina por Imunoprecipitação
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article