chirpseq-analysis

This is a set of scripts that together convert ChIRP-seq (chromatin immunoprecipitation followed by RNA purification and sequencing) fastq files into plots and bedgraphs suitable for downstream processing by metagene-maker.

Some of these scripts were authored by Kun Qu.

Usage

runchirp.sh <organism> <name> <even fastq> <odd fastq> <removal bed file>

Example: runchirp.sh human A375 even_trimmed.fastq odd_trimmed.fastq human_7sk.bed

Required arguments:

position	description
organism	either 'human' or 'mouse'. These are the only two supported at the moment.
name	User-specified prefix for all output files
even fastq, odd fastq	TRIMMED fastq file
removal bed file	genomic positions of the RNA loci that must be masked

Installation instructions and dependencies

• Clone this repository by running one of the following:

  • git clone git@github.com:bdo311/chirpseq-analysis.git if you use ssh authentication
  • git clone https://github.com/bdo311/chirpseq-analysis.git otherwise

• Dependencies

  • Bowtie2 (mapping): http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
  • MACS 1.4 (peak finding): http://liulab.dfci.harvard.edu/MACS/
  • Samtools (genome manipulation): http://samtools.sourceforge.net/
  • Bedtools (genome arithmetic): http://bedtools.readthedocs.org/en/latest/
  • Python (helper code): https://www.python.org/download/releases/2.7/
  • R (plots): http://www.r-project.org/

Input

2 FASTQ files (even and odd replicates). These FASTQ files must be trimmed (5' and 3'), quality filtered, and collapsed prior to running ChIRPseq analysis.

Output

• normalized bedgraphs for repeat-mapped and genome-mapped reads
• bw file for genome mapped reads
• plots for ChIRP coverage of repeat RNAs
• peak bed file for genome ChIRP