A benchmark of computational pipelines for single-cell histone modification data.

ABSTRACT:

Background

Single-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues and are likely to unlock our understanding of various mechanisms involved in development or diseases. Running scHTPM experiments and analyzing the data produced remains challenging since few consensus guidelines currently exist regarding good practices for experimental design and data analysis pipelines.

Results

We perform a computational benchmark to assess the impact of experimental parameters and data analysis pipelines on the ability of the cell representation to recapitulate known biological similarities. We run more than ten thousand experiments to systematically study the impact

SUBMITTER: Raimundo F 

PROVIDER: S-EPMC10280832 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature