A program for calculating enriched structural motifs using constraints from RNA proximity ligation experiments.
RNA proximity ligation methods such as CLASH, HiC, PARIS, SPLASH, and COMRADES generate chimeric reads that represent RNA-RNA interactions.
Structural_motifs inputs a tab-delimited file with chimeric reads (with the sequences of arms 1 and 2 of each chimera in separate columns), and outputs a graph with structural motif enrichments
Linux operating system
UNAFold http://unafold.rna.albany.edu/?q=DINAMelt/software
bedtools v2.16.2
# clone package using git:
git clone https://github.com/gkudla/structural_motifs.git
Add installation location to your PATH:
export PATH="path-to-installation-folder/structural_motifs/bin:$PATH"
To test the program, copy the example input file from structural_motifs/data into a folder of your choice, then run the commands below. Typical run time on the test data is less than 1 minute
structural_motifs USA300_RNaseIII_RPMI_JOIN_intermolecular_hybs_filtered.txt
# plot with structural motif frequencies on the X axis and motif enrichment on the Y axis
JKD_RNaseY_RPMI_JOIN_intermolecular_hybs_filtered.pdf
- Grzegorz Kudla, 2020
This project is licensed under the GNU General Public License v3 - see the LICENSE.md file for details