This repository provides a tool to analyze and output significant inter-chromosomal interactions of a given dataset.
To run the tool on the oocyte_NSN data, execute the following command from the project home directory:
python src/main.py --data "sample-data/data" --bin-size "500k" --config-file "metadata/mm9_chrom_sizes.txt" --output "sample-data/output_oocyte_NSN_500k.txt"
Above command provides the bin size as 500,000.
You can check out the other options available to use with the tool using:
python src/main.py --help
The supported input format is a list of files consists of links. Each file should have the format:
chromosome_1 coordinate_1 chromosome_2 coordinate_2 weight
The output file lists n significant inter chromosomal interactions identified. The n lines are as follows:
bin_1 bin_2 count p_value
where bins are represented as the size given in the input command.