Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.
Genome Biol
; 23(1): 119, 2022 05 24.
Article
em En
| MEDLINE
| ID: mdl-35606795
ABSTRACT
BACKGROUND:
The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq). A large number of algorithms and computational tools for quantitative comparison of ChIP-seq datasets exist, but their performance is strongly dependent on the parameters of the biological system under investigation. Thus, a systematic assessment of available computational tools for differential ChIP-seq analysis is required to guide the optimal selection of analysis tools based on the present biological scenario.RESULTS:
We created standardized reference datasets by in silico simulation and sub-sampling of genuine ChIP-seq data to represent different biological scenarios and binding profiles. Using these data, we evaluated the performance of 33 computational tools and approaches for differential ChIP-seq analysis. Tool performance was strongly dependent on peak size and shape as well as on the scenario of biological regulation.CONCLUSIONS:
Our analysis provides unbiased guidelines for the optimized choice of software tools in differential ChIP-seq analysis.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Sequenciamento de Cromatina por Imunoprecipitação
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Genome Biol
Assunto da revista:
BIOLOGIA MOLECULAR
/
GENETICA
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Áustria