Example1: Testing if one TAD is reorganized

In this example, we tested the GM12878 TAD that is reorganized in K562 (Chr1:163500000-165000000, Ref). Data are saved in <data/single-TAD/>.

Running the command

• Usage: scriptname dvsd one <chr> <start> <end> <hic0> <hic1> [options]

python diffdomain-py3/diffdomains.py dvsd one 1 163500000 165000000 \
data/GSE63525_GM12878_insitu_primary_replicate_combined.hic \
data/GSE63525_K562_combined.hic \
--reso 10000 \
--ofile output/example1_chr1_163500000_165000000.txt

If the input is cool or mcool file, the usage is the same.