MultiRepMacsChIPSeq

A multi-threaded wrapper for processing multi-replicate, multi-condition ChIPSeq samples

Description

ChIPSeq and related methods, such as ATACSeq, is increasingly being used not just as a means of discovery (“where is my factor binding?”) but also as an assay for experimental conditions (“how does my mutant affect factor X occupancy?”). Many traditional ChIPSeq programs are not necessarily well equipped to handle multiple replicates and/or sample conditions.

This is a wrapper application for processing ChIPSeq samples comprised of multiple biological replicas and/or multiple conditions in a manner to make comparisons as consistent and uniform as possible across samples.

Rationale

The venerable MACS2 application provides a robust method of determining enrichment of ChIP fragments over input with a number of advantages: fragment-based pileup of ChIP signal versus simple counts, single base-pair resolution instead of sliding windows, estimation of local chromatin bias using multiple window sizes, and more. However, Macs2 does not natively deal with replicates, and comparing multiple conditions requires careful, manual execution of each set with identical parameters and/or complicated intersections.

This package aims to automate Macs2 ChIPSeq peak calling with support for multiple replicas and conditions while supporting newer normalization methods. Importantly, it will output normalized, processed bigWig enrichment files for subsequent genic analysis; numerous analytical, comparative, and quality contrrol metric plots; and peak count tables ready for quantitative differential analysis. Finally, an overview HTML report is generated with tables of numbers and selected QC and analytical plots.

NOTE This project currently uses MACS version 2. While MACS3 has been released, it has not yet been evaluated and incorporated into this pipeline.

Overview

See the overview page for a description of the steps involved in the pipeline.

Installation

See the accompanying Installation guide for detailed notes on getting the pipeline setup.

Users at HCI running the pipeline on local Linux servers can simply load the packages into your environment using a module command.

module load multirepchipseq

This is also installed at CHPC at the University of Utah; please contact the Cancer Bioinformatics shared resource for details.

Usage

See the Usage Guide for detailed notes on how to run the pipeline. For variations in running the pipeline, such as with ATAC-Seq or Cut & Run, see the variations page.

A full list of application menus is available.

See the examples page for using the pipeline in common scenarios.

AUTHOR

Timothy J. Parnell, PhD
Cancer Bioinformatics Shared Resource
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

LICENSE

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0. For details, see the full text of the license in the file LICENSE.

This package is distributed in the hope that it will be useful, but it is provided “as is” and without any express or implied warranties. For details, see the full text of the license in the file LICENSE.