A unified caller for TADs and stripes in various Hi-C data
Dependencies:
pip install numba
pip install numpy
pip install scipy
pip install sklearn
pip install qpsolvers==1.10.0
Go to the repository of this folder
Test run:
Single sample run:
python JOnTADS.py -F ./data/chr18.csv -O ./results/chr18.csv.tad
Multiple samples run:
python JOnTADS.py -F ./data/ES_rep1.chr18 ./data/ES_rep2.chr18 ./data/ME_rep1.chr18 ./data/ME_rep2.chr18 ./data/MS_rep1.chr18 ./data/MS_rep2.chr18 ./data/NP_rep1.chr18 ./data/NP_rep2.chr18 ./data/TP_rep1.chr18 ./data/TP_rep2.chr18 -O ./results/ES_rep1.chr18.tad ./results/ES_rep2.chr18.tad ./results/ME_rep1.chr18.tad ./results/ME_rep2.chr18.tad ./results/MS_rep1.chr18.tad ./results/MS_rep2.chr18.tad ./results/NP_rep1.chr18.tad ./results/NP_rep2.chr18.tad ./results/TP_rep1.chr18.tad ./results/TP_rep2.chr18.tad
Stripe calling:
python get_stripe.py -F ./data/chr18.csv -O ./results/chr18.csv.stripe -C 18