Example2: Testing TADs on all chromosomes

Data is using Amazon.

• Identify TADs in multiple chromosomes simultaneously.

python diffdomain-py3/diffdomains.py dvsd multiple https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined.hic data/GSE63525_GM12878_primary+replicate_Arrowhead_domainlist.txt --ofile res/temp/temp.txt

• MultiComparison adjustment.

python diffdomain-py3/diffdomains.py adjustment fdr_bh res/temp/GM12878_vs_K562_chr1_50M_temp.txt res/adjusted_TADs2.txt 

• optional parameter [--filter], Filtering out reorganized TADs with BH < 0.05.

python diffdomain-py3/diffdomains.py adjustment fdr_bh res/temp/GM12878_vs_K562_chr1_50M_temp.txt res/reorganized_TADs_GM12878_K562.tsv --filter true

The final output is saved to <res/reorganized_TADs_GM12878_K562.tsv>.

• Classification of TADs

In this step, you will need the tadlist of the second hic file.

Running the command:

python diffdomain/classificattion.py -d adjusted_TADs2.txt -t GSE63525_K562_Arrowhead_domainlist.txt