Unsupervised Contrastive Peak Caller for ATAC-seq.

ABSTRACT: The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing. These sequenced regions are quantified and tested for enrichment in a process referred to as "peak calling". Most unsupervised peak calling methods are based on simple statistical models and suffer from elevated false positive rates. Newly developed supervised deep learning methods can be successful, but they rely on high quality labeled data for training, which can be difficult to obtain. Moreover, though biological replicates are recognized to be important, there are no established approaches for using replicates in the deep lea

SUBMITTER: Vu HTH 

PROVIDER: S-EPMC9881890 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature