Computational Regulatory Genomics

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PARpipe is a complete analysis pipeline for PAR-CLIP data providing the following features:

  • Pre-processing and alignment of reads
  • Definition of interaction sites using PARalyzer v1.5
  • Additional site-level metrics
  • Annotation of reads, groups, and cluster
  • Meta-analysis of binding sites relative to important transcript features

PARpipe is housed at github:

We have provided support for both human and mouse datasets and it can be modified for other organisms.

The github repository includes PARalyzerv1.5.

Additionally we provide an  script "" in the github repository that will automatically download all necessary accesory files for human hg19 and/or mouse mm10 genomes and put these files in the proper location. These include bowtie genome indices, .2bit genomes, and annotation (gencode and repeat)...Alternatively, the user can prepare this on their own.

It has been tested on linux systems. There may be difficulties on mac os/x.

It has the following software dependencies (tested version), for which users must either add the executable to their path or specify the path at the top of the script.

Bpipe (

Bowtie (0.12.7)

SAMtools (0.1.17)

BEDtools (v2.20.1)

cutadapt (1.3) 

In this example PARpipe will be installed in the home directory, see README for more information.


# This will create a directory PARpipe/ in your home directory containing everything you need to setup and run PARpipe.
git clone

cd PARpipe

# If you want to download all necessary files for analysis of human -hg19 and/or mouse -mm10 data (this is all we support at the moment).

# bash -s <h|m|b>
# h = human, m = mouse, b = human and mouse
bash -s h

# To test PARpipe, go to the PARpipe/test directory
cd test
bpipe run -r ../ test.fastq

#to remove unnecessary intermediates:
bpipe preserve *.csv *.bed *.distribution *.bam *.bam.bai *.clusters.txt *ini *pdf
bpipe cleanup -y



Below are links to additional files. If you run the script you will alread have these!

Human (hg19):

 Mouse (mm10):


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