Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.

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 profile

SUBMITTER: Eder T 

PROVIDER: S-EPMC9128273 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature