Complementary Sequence Index (CSI) is pipeline to quantitate RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns.
git clone https://github.com/YangLab/CSI
python ./setup.py installusage: 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.
CSI -g hg19.fa test_circ.txt -o test_circ_csi -p 10- circ_file is in the format of output of CIRcexplorer/CIRCexplorer2.
- hg19.fa is genome sequence in FASTA format.
- 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 |
Dong R*, Ma XK*, Chen LL# and Yang L#. Increased complexity of circRNA expression during species evolution. RNA Biol, 2016 (Accepted)
Copyright (C) 2016 YangLab. See the LICENSE file for license rights and limitations (MIT).