integrated Genome-Wide Off-target cleavage Search platform
iGWOS is designed for the optimal genome-wide off-target sites (OTS) prediction by integrating the available OTS prediction tools in a complementary way. iGWOS integrates OTS prediction tools with an Adaboost framework, supports conventional NGG-PAM OTS prediction with mismatches up to 6 in human species.
iGWOS searches the candidate off-target sites with Cas-OFFinder and predict CRISPR/Cas9-induced off-target cleavage sites by integrating distinct OTS prediction tools (CRISPRoff, uCRISPR, DeepCRISPR, CFD, MIT, CROP-IT and CCTop). The genome encode way can be referred to DeepCRISPR (https://github.com/bm2-lab/DeepCRISPR)
By inputting the gRNA(s) sequence file and related restrictions, iGWOS precisely predicts the genome-wide OTS list of given gRNAs, and visualizes the top 200 risky genome-wide off-target profile with a Circos plot. The iGWOS score of a off-target site denotes its cleavage probability.
- python==3.7
- pandas==0.20.1
- numpy==1.14.5
- pyfaidx==0.4.8.4
- tensorflow==1.8.0
- sonnet==1.33
- uCRISPR==0.1
- RNAstructure==6.2
- python==2.7
- biopython==1.73
- ViennaRNA==2.4.12
- RIsearch==2.1
- circos==0.69-6
-
git clone https://github.com/bm2-lab/iGWOS.git
-
Install the dependency:
# pull the image from Docker Hub $ docker pull jafferyan/igwos_1.0:latest
python3 main.py [-h] [-v] [-gRNA GRNA] [-g GENOME] [-m {0,1,2,3,4,5,6}]
[-cell CELL] [-cid CID] [-e ENCODE] [-circos {0,1}] [-gpu GPU]
[-o OUTPUT]
Predict genome-wide CRISPR-Cas9 off-target sites with iGWOS.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-gRNA GRNA gRNAs file in Fasta format
-g GENOME genome folder for candidate off-target searching,
default=genome/hg19
-m {0,1,2,3,4,5,6} maximum mismatch allowed in off-target prediction,
default=5
-cell CELL cell-type of gRNAs
-cid CID cell-id file, formed like data/encode_hg19.tab
-e ENCODE epigenomic encode folder, default=/data/genome/encode/fa/
-circos {0,1} whether to draw a circos plot to visualize the top 200
risky predicted off-target profile, default=1
-gpu GPU select a gpu device to perform cas-offinder and/or
deepcrispr, default=0
-o OUTPUT output folder, default=output/
python3 main.py -gRNA data/grna.fa -g genome/hg19 -m 5 -cell K562 -cid data/encode_hg19.tab -e /data/genome/encode/fa/ -circos 1 -gpu 1 -o output
gRNA file format
>sg1
GCCTCCCCAAAGCCTGGCCAGGG
>sg2
GGCCAGGCTTTGGGGAGGCCTGG
cell-id file format: [cid] [cell]
h1 MCF-7
h2 GM12878
h3 HepG2
h4 LNCaP clone FGC
h5 HCT116
h6 HeLa-S3
h7 K562
encode folder format (take K562 cell as an example)
Format: [encode_path]/[cid]_[epi].fa
/data/genome/encode/fa/h7_ctcf.fa
/data/genome/encode/fa/h7_dnase.fa
/data/genome/encode/fa/h7_h3k4me3.fa
/data/genome/encode/fa/h7_rrbs.fa
output format
sgID gRNA OTS Chr Strand Start Mismatch iGWOS
sg1 GCCTCCCCAAAGCCTGGCCAGGG GCCTCCCCAAAAGCTGAGCAGGG chr1 + 929401 4 0.3254589692131059
sg1 GCCTCCCCAAAGCCTGGCCAGGG TGCTCCCCAGAGCCTAGCCGTGG chr7 - 1900836 5 0.46115958387343875
sg1 GCCTCCCCAAAGCCTGGCCAGGG ACCTCCCCATAGCCTGGCCAGGG chr11 - 44986455 2 0.529510001952807
OTS Circos visualization format
Yan, J., Liu, Q., et al. (2020). "Benchmarking and integrating genome-wide CRISPR off-target detection and prediction." Nucleic Acids Res 48(20): 11370-11379.