Dataset Information

snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis.

ABSTRACT:

Summary

Genome-wide chromosome conformation capture (Hi-C) is a technique that allows the study of 3D genome organization. Despite being widely used, analysis of Hi-C data is technically challenging and involves several time-consuming steps that often require manual involvement making it error prone, potentially affecting data reproducibility. In order to facilitate and simplify these analyses we implemented snHiC, a snakemake-based pipeline that allows for the generation of contact matrices at multiple resolutions in one single run, aggregation of individual samples into user-specified groups, detection of domains, compartments, loops and stripes and performance of differential compartment and chromatin interaction analyses.

Availability and implementation

Source code is freely available at https://github.com/sebastian-gregoricchio/snHiC. A yaml-formatted file (snHiC/workflow/envs/snHiC_conda_env_stable.yaml) is available to build a compatible conda environment.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

SUBMITTER: Gregoricchio S

PROVIDER: S-EPMC10307938 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

<i>snHiC</i>: a complete and simplified snakemake pipeline for grouped Hi-C data analysis.

Gregoricchio Sebastian S Zwart Wilbert W

Bioinformatics advances 20230621 1

<h4>Summary</h4>Genome-wide chromosome conformation capture (Hi-C) is a technique that allows the study of 3D genome organization. Despite being widely used, analysis of Hi-C data is technically challenging and involves several time-consuming steps that often require manual involvement making it error prone, potentially affecting data reproducibility. In order to facilitate and simplify these analyses we implemented <i>snHiC</i>, a snakemake-based pipeline that allows for the generation of conta ...[more]

PMID: 37397353

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