circRCM_knockout

Script that produces BED files of RCMs

Installation

To install run this in the terminal:

git clone https://github.com/alexandruioanvoda/circRCM_knockout
cd ./circRCM_knockout
chmod +x ./*

The installation and runs were tested on Ubuntu 18

The following dependencies need to be installed: Python 3, biopython, bedtools Also, the ce11 genome needs to be downloaded in the circRCM_knockout folder. This terminal one-liner will do it: wget -c http://hgdownload.cse.ucsc.edu/goldenPath/ce11/bigZips/chromFa.tar.gz -O - | gzip -dc | tar -xO > ce11.fa

For any issues running scripts in this repository, please email at [email protected]

Run

Navigate with the terminal to the circRCM_knockout folder and run:

python Script.py

Input

Just insert the coordinates of the introns flanking the circRNA. Example: for Circ_0000333, chrIII, +, 1927947, 1929102, 1918723, 1927649 (chromosome in ce11 genome, strand, intron 1 start, intron 1 end, intron 2 start, intron 2 end)