tad_compare

Is a python library to compare different sets of TADs (or CCDs) inferred from 3D genomic data (Hi-C, ChIA-PET or other 3C techniques).

It's still under development, current version supports comparing multiple different sets of TADs saved in separate .bed files.

BED file format requires information about chromosome in first column and about TAD start and end in second and third column respectively. Other columns are ignored at this stage.

EXAMPLE:

chr1 40000 200000
chr1 880000 1320000
chr1 1920000 2400000
chr1 2400000 2480000
chr1 2760000 3440000
....

Measure of Concordance (MoC)

Parameteres:

-h, --help show this help message and exit
-a BEDFILE_1, --bedfile_1 Bedfile with first set of domains or path to multiple domains files.
-b BEDFILE_2, --bedfile_2 Bedfile with second set of domains. Used only if --bedfile_1 is not a directory.
-o OUTPUT, --output Directory to save output file. Output is saved only when analysing multiple sets of TADs (When --bedfile_1 is a directory). If None save in input directory.
-r REPORT, --report If True return MoC to stdout. Default=True

Comparing two sets:

Usage:

./moc.py -a domains_to_compare/NA19238_all_domains.bed -b domains_to_compare/NA19239_all_domains.bed

Output:

Number of domains in NA19238_all_domains: 3918
Number of domains in NA19239_all_domains: 3871
MoC for NA19238_all_domains and NA19239_all_domains equals to: 0.847649147998292

Comparing multiple sets:

Usage:

./moc.py -a ~/domains_to_compare/ -o output.csv -r True

Output:

Measure of Concordance is implemented according to formula proposed in:

Zufferey, Marie, et al. "Comparison of computational methods for the identification of topologically associating domains." Genome biology 19.1 (2018): 217.

Conserved domains

Parameteres:

-h, --help show this help message and exit
-a BEDFILE_1, --bedfile_1 Bedfile with first set of domains or path to multiple domains files.
-b BEDFILE_2, --bedfile_2 Bedfile with second set of domains. Used only if --bedfile_1 is not a directory.
-o OUTPUT, --output Directory to save output file. Output is saved only when analysing multiple sets of TADs (When --bedfile_1 is a directory. If None save in input directory.
-r REPORT, --report If True print output matrix to stdout. Default=True
-s SHIFT, --shift Accepted shift of two domain boundaries positions in base pair.

Comparing two sets:

Usage:

./common_tads.py -a NA19238_all_domains.bed -b NA19240_all_domains.bed

Output:

Number of common TADs between NA19238_all_domains and NA19240_all_domains with shift 0 bp equals to: 1287.'

Comparing multiple sets:

Usage:

./common_tads.py -a ~/domains/yoruba/ -o ./readme_example/common_tads.csv -r True -s 0

Output:

Venn diagram

Plot Venn diagram of TADs shared among either two or three different sets.

Two sets:

Usage: ./plot_venn.py -d NA19239_all_domains.bed NA19240_all_domains.bed -o ./readme_example/venn_2_sets.png

Output:

Three sets:

Usage:

./plot_venn.py -d NA19239_all_domains.bed NA19240_all_domains.bed NA19238_all_domains.bed -o ./readme_example/venn_3_sets.png

Output: