CSI

Complementary Sequence Index (CSI) is pipeline to quantitate RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns.

Schema

Requirements

• blastn (>=2.2.30+)
• pysam (>=0.8.4pre)

Installation

git clone https://github.com/YangLab/CSI
python ./setup.py install

Usage

usage: CSI [-h] [-v] -g GENOME [-l LENGTH] [-p THREAD] [-o OUTPUT] [--tmp]
           circ_file

positional arguments:
  circ_file             The circular RNA file (CIRCexplorer format)

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -g GENOME, --genome GENOME
                        Genome fasta file.
  -l LENGTH, --length LENGTH
                        Minimum pair length. [default: 50]
  -p THREAD, --thread THREAD
                        Running threads. [default: 10]
  -o OUTPUT, --ouput OUTPUT
                        Output file. [default: circ_cs]
  --tmp                 Keep temporary BLAST results.

Example

CSI -g hg19.fa test_circ.txt -o test_circ_csi -p 10

Note

• circ_file is in the format of output of CIRcexplorer/CIRCexplorer2.
• hg19.fa is genome sequence in FASTA format.

Output

• test_circ_csi.txt

Field	Description
chrom	Chromosome
start	Start of junction
end	End of junction
CSI	The max CSI score among CSs of the circRNA
left region	The left pair region
right region	The right pair region

Citation

Dong R*, Ma XK*, Chen LL# and Yang L#. Increased complexity of circRNA expression during species evolution. RNA Biol, 2016 (Accepted)

License

Copyright (C) 2016 YangLab. See the LICENSE file for license rights and limitations (MIT).