1. Introduction

ChIRP-seq Analysis Pipeline intergrates several DNA sequence tools and is used particularly to analyze ChIRP-seq data. 
The input files are "even_lane.fastq", "odd_lane.fastq" and "input_lane.fastq", with an output table that one can used to filter true peaks based on fold change, fdr, pearson correlation between even and odd lanes, fold difference between even and odd lanes, and everage coverage etc.

This pipeline is developed by Kun Qu in Stanford School of Medicine


2. Pre-requisite:

a. Bowtie alignment tool installed, please see the instructions here:
http://bowtie-bio.sourceforge.net/index.shtml

b. MACS peak caller installed, please see the instructions here:
http://liulab.dfci.harvard.edu/MACS/index.html

c. UCSC file converte excutables, one can download from here:
http://hgdownload.cse.ucsc.edu/admin/exe/
depending on what system you are using


3. Install

a. Unpack the tarball:
tar -zxvf chirpseq.tar.gz

b. Edit the "config.txt" file, and give FULL path of each excutables, and make sure those pathes are in your bashrc/bash_profile file


4. Run the pipeline:

perl chirp_seq.pl -c config.txt -o output.txt 
