PARpipe
Deciphering human ribonucleoprotein regulatory networks
Publication:
N. Mukherjee, HH. Wessels, S. Lebedeva, M. Sajek, M. Ghanbari, A. Garzia, A. Munteanu, D. Yusuf, T. Farazi, J. I Hoell, K. M Akat, A. Akalin, T. Tuschl, U. Ohler (2018): Deciphering human ribonucleoprotein regulatory networks Nucleic Acid Research
About:
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
Repository:
PARpipe is housed at github:
https://github.com/ohlerlab/PARpipe
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 "setup.sh" 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 parpipe.sh script.
Bpipe (0.9.8.5)
Bowtie (0.12.7)
SAMtools (0.1.17)
BEDtools (v2.20.1)
cutadapt (1.3)
QUICK START:
In this example PARpipe will be installed in the home directory, see README for more information.
cd
# This will create a directory PARpipe/ in your home directory containing everything you need to setup and run PARpipe.
git clone https://github.com/ohlerlab/PARpipe.git
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 setup.sh -s <h|m|b>
# h = human, m = mouse, b = human and mouse
bash setup.sh -s h
# To test PARpipe, go to the PARpipe/test directory
cd test
bpipe run -r ../parclip_pipe.sh 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 setup.sh script you will alread have these!
Human (hg19):
- bowtie indices (these will need to be unzipped)
- 2BIT genome
- GTF also available at GENCODE
- repeat masker files (these will need to be unzipped)
- example fastq data
- HEK293 expresssion gtf
Mouse (mm10):
- bowtie indices (these will need to be unzipped)
- 2BIT genome
- GTF also available at GENCODE
- repeat masker files (these will need to be unzipped)