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.
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
| 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 |
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Clone this repository by running one of the following:
git clone git@github.com:bdo311/chirpseq-analysis.gitif you use ssh authenticationgit clone https://github.com/bdo311/chirpseq-analysis.gitotherwise
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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/
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.
- 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