comrades

A program for folding RNA using constraints from proximity ligation experiments.

Background

RNA proximity ligation methods such as CLASH, HiCLIP, PARIS, SPLASH, and COMRADES generate chimeric reads that represent RNA-RNA interactions.

Comrades inputs a set of mapped chimeric reads (produced by hyb, https://github.com/gkudla/hyb), and outputs a ranked list of predicted basepairs. It then combines these basepairs into short structural elements, ranks the elements by number of supporting chimeric reads, and uses the ranked elements as constraints for RNA folding. The output is an RNA structure or set of structures in UNAFold .ct format or vienna dot-bracket format.

Prerequisites

Linux operating system

Perl version 5

UNAFold http://unafold.rna.albany.edu/?q=DINAMelt/software

Installation

# download package:
wget https://github.com/gkudla/comrades/archive/master.zip
unzip master.zip
mv comrades-master/ comrades

# or clone using git:
git clone https://github.com/gkudla/comrades.git

Add installation location to your PATH:

export PATH=comrades/bin:$PATH

Running the scripts

To test the programs, first copy the example input files from comrades/data into a folder of your choice, then run the commands below. Typical run time on the test data is 1 minute for comradesMakeConstraints, and 7 minutes for comradesFold.

generate folding constraints

comradesMakeConstraints -i testData.hyb -f Zika.fasta -b 3324 -e 4521

fold RNA using constraints

comradesFold -c testData.3324-4521_folding_constraints.txt -i Zika_3324-4521.fasta

fold RNA 1,000 times (requires computer cluster running qsub)

qsub comradesFold -c testData.3324-4521_folding_constraints.txt -i Zika_3324-4521.fasta -s 1

Outputs

# input folding constraints: 
testData.3324-4521_folding_constraints.txt

# a subset of mutually compatible folding constraints used to generate the folded structure:
testData.3324-4521_folding_constraints.txt.accepted

# folded RNA in hybrid-ss-min .ct format:
Zika_3324-4521.fasta.ct

# folded RNA in vienna dot-bracket format:
Zika_3324-4521.fasta.vienna

Authors

Grzegorz Kudla, Marta Gabryelska 2018

License

This project is licensed under the GNU General Public License v3 - see the LICENSE.md file for details

gkudla / comrades

readme