Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes.

ABSTRACT:

Background

ChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task.

Results

This study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by

SUBMITTER: Sharma V 

PROVIDER: S-EPMC7035708 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature