ChipSeqFall2013

= ChIP-Seq NGS Data Analysis =

October 14, 2013


__**Tools**__**:**

A widely-used, fast, robust ChIP-seq peak-finding algorithm.
 * MACS **

A ChIP-seq peak calling algorithm, implemented as an R package.
 * SPP **

An open, web-based platform with some useful tools for ChIP-Seq data analysis.
 * GALAXY **

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.
 * CISTROME **

__**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 **