MACS
A widely-used, fast, robust ChIP-seq peak-finding algorithm.
SPP
A ChIP-seq peak calling algorithm, implemented as an R package.
GALAXY
An open, web-based platform with some useful tools for ChIP-Seq data analysis.
CISTROME
The Cistrome AP module organizes analysis tools in a pipeline for users, and provides users a dry-lab workbench for them to process their own private data.
ChIP-Seq NGS Data Analysis
Instructor: Chitra Kotwaliwale (chitra.kot@gmail.com)
March 18, 2013
Tools:
MACS
A widely-used, fast, robust ChIP-seq peak-finding algorithm.
SPP
A ChIP-seq peak calling algorithm, implemented as an R package.
GALAXY
An open, web-based platform with some useful tools for ChIP-Seq data analysis.
CISTROME
The Cistrome AP module organizes analysis tools in a pipeline for users, and provides users a dry-lab workbench for them to process their own private data.
Relevant papers:
This paper discusses GC and other biases in high-througput sequencing
Paper by Liu and colleagues describing MACS
Detailed "protocol" for how to install and use MACS
ChIP-Seq guidles outlined by ENCODE and modENCODE
Paper by Kharchenko and colleagues describing spp
Useful Links:
Information about file formats