Benchmarking of 4C-seq pipelines based on real and simulated data.

ABSTRACT:

Motivation

With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data are complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published.

Results

We conducted a benchmarking study on 66 4C-seq samples from 20 datasets, and developed a novel 4C-seq simulation software, Basic4CSim, to allow for detailed compariso

SUBMITTER: Walter C 

PROVIDER: S-EPMC6901067 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature