JOnTADS 0.9

JOnTADS: a unified caller for TADs and stripes in Hi-C data

JOnTADS: a unified caller for TADs and stripes in Hi-C data

JOnTADS is a versatile tool for identifying Topologically Associating Domains (TADs) and stripes in various chromatin conformation capture data, including population Hi-C, single-cell Hi-C and micro-C. It allows for easy analysis of Hi-C data across multiple samples.

Dependencies

pip install numba==0.56.4  
pip install numpy==1.23.5  
pip install scipy==1.12.0  
pip install qpsolvers==2.7.3

Installation

pip install JOnTADS

Test Run

Suppose you are at the folder of this README file.

Single Sample Run

To identify TADs from a single sample, use the following command:

JOnTADS -F ./data/chr18.csv -O ./results/chr18.csv.tad

Multiple Samples Run

To analyze multiple samples simultaneously, use:

JOnTADS -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

To call stripes in addition to TADs:

JOnTADS -F ./data/chr18.csv -O ./results/chr18.csv.tad --stripe True --stripe_output ./results/chr18.csv.stripe --chr 18

Usage

You can run JOnTADS in your terminal via

JOnTADS -F ./data/chr18.csv -O ./results/chr18.csv.tad --stripe True --stripe_output ./results/chr18.csv.stripe --chr 18

or

python JOnTADS.py -F ./data/chr18.csv -O ./results/chr18.csv.tad --stripe True --stripe_output ./results/chr18.csv.stripe --chr 18

or in your python file via

from JOnTADS import JOnTADS, get_stripe
tads = JOnTADS(file_names, outputs)
stripes = get_stripe(file_name, chr_num)

Input and Output Format

Input Format

The input files should be Hi-C contact matrices separated by spaces or commas.

In progress: we are working on supporting supporting additional input formats.

Output Format

The output files contain information about the identified TADs or stripes.

For TAD calling, the output contains four columns:

start, end, TAD score, TAD size

For stripe calling, the output contains six columns

chr, x1, x2, chr, y1, y2

where the stripe extends from (x1, y1) to (x2, y2).

Parameters

• -F: Input file(s) with Hi-C data.
• -O: Output file(s) for the detected TADs.
• -MAXSZ: Maximum size of TADs allowed, default 200.
• -MINSZ: Minimum size of TADs allowed, default 7.
• --stripe: Set to True to enable stripe detection.
• --chr: (When `stripe' is set to True) Chromosome number for stripe calling, e.g. 18.
• --stripe_output: (When `stripe' is set to True) Output file for stripe calling results.

Contact

Feel free to contribute to the project by opening issues or pull requests. Any feedback or suggestions are highly appreciated. Correspondence should be addressed to [e-mail]. You can also contact the maintainer [e-mail].

Happy analyzing your Hi-C data with JOnTADS!