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

Publikationen als Autor:in / Herausgeber:in der Vetmeduni

Grebien, Florian; Eder, Thomas

Abstrakt

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.

Dokumententyp

Originalarbeit

Open Access Type

Gold

DOI

10.1186/s13059-022-02686-y

PubMed ID

MEDLINE:35606795

Projekt

Common Oncogenic Mechanisms in Multi-Partner Translocation Families in Acute Myeloid Leukemia; Non-coding RNAs in oncogene-induced biomolecular condensates