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Tian-Dechao / diffDomain

DiffDomain is a statistically sound method for detecting differential TADs between conditions
MIT License
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File input for Diffdomain #10

Closed FlavianR closed 1 year ago

FlavianR commented 1 year ago

Hi! Thanks for this tool! I have a question about the format of input file. Only file.hic are accepted ? Or can we use an other format (like cool or mcool) with a trick ? If not are you planning to add more format possibilities or to stay with only the hic format ?

Thank you in advance for your answers.

Tian-Dechao commented 1 year ago

Thanks for this great comment! A quick response first. 1 Yes, only file .hic are supported now. 2 But there is a trick to work with other format. Specifically, the straw function can be replaced with equivalent functions to extract the contact matrices from other formats and save them in 2D np.array format (N by N). After that, the rest code should run smoothly. 3 Other format (like cool or mcool) will be directly supported in about one-week time. Please stay tuned.

mingbao96 commented 1 year ago

Hi, @FlavianR, thank you for your interest in DiffDomain! We have updated DiffDomain to directly support input Hi-C data in .cool and .mcool file formats in addition to .hic. You can now use these formats for input as well. For details, please see our description of Hi-C data.

To use the updated DiffDomain code, please either download the updated diffdomain-py3 folder [link] from GitHub or update to the latest version (0.2.1) using pip install diffDomain-py3==0.2.1 to access this new feature.

Let me know if you have any more questions or encounter any issues. Thanks again for using DiffDomain!

FlavianR commented 1 year ago

Thanks for this update!