ROCCO: a robust method for detection of open chromatin via convex optimization.

ABSTRACT:

Motivation

Analysis of open chromatin regions across multiple samples from two or more distinct conditions can determine altered gene regulatory patterns associated with biological phenotypes and complex traits. The ATAC-seq assay allows for tractable genome-wide open chromatin profiling of large numbers of samples. Stable, broadly applicable genomic annotations of open chromatin regions are not available. Thus, most studies first identify open regions using peak calling methods for each sample independently. These are then heuristically combined to obtain a consensus peak set. Reconciling sample-specific peak results post hoc from larger cohorts is particularly challenging, and informative spatial features specific to open chromatin signals are not leveraged effectively.

Result

SUBMITTER: Hamilton NH 

PROVIDER: S-EPMC10715771 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature