HiCPro output format?

Juan A Rodriguez

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Oct 13, 2022, 8:58:01 AM10/13/22

to HiC-Pro

Hi,

I am trying to run a software that takes as input the *.matrix and *.bed files out from HiCPro.

I simply would like to know whether the format I am using for my HiC data(see screenshot attached) is the correct one, both for the matrix and the bed, that would be expected to get from HiCPro. It is a full upper matrix with all pairs, even those that are 0 for interaction frequency, plus a bed file with all the coordinates.

I tried to download your test data from the "zerkalo" repository to see if I could mimic it , but the connection seems broken.

Hope you can help here!

Thanks,

Juan

Screenshot 2022-10-13 at 14.50.51.png

nservant

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Oct 14, 2022, 4:40:52 AM10/14/22

to HiC-Pro

Hi,

Yes it looks good. Of note, this is not a full upper matrix, as you should not have the 0s.

Sorry for Zerkalo ... that's an old server, and it seems that the last version of web browsers do not support the certificates (which are two old I guess)

Sometimes you can force the access, depending on the web browser.

Best

Nicolas

Juan A Rodriguez

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Oct 14, 2022, 4:48:38 AM10/14/22

to HiC-Pro

Dear Nicolas,

Thank you for your quick answer!

I have already been able to read the files into that other program. Turns out it was a bug on their side...

Still, do you suggest I should remove the interaction pairs with 0 contacts, to make my file the most similar to the HiCPro output?

Thanks again!

Best,

Juan

nservant

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Oct 14, 2022, 4:53:13 AM10/14/22

to HiC-Pro

In theory, it should not be an issue, as soon as you have the same bins information in the matrix/bed files.

However, I just wondering if the different programs loading these files will still consider the input data as sparse matrix if you have the zeros.

If the data are loaded as dense matrix (and not sparse), you may have some memory issue for high resolution data ...

Best

Juan A Rodriguez

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Oct 14, 2022, 4:55:56 AM10/14/22

to nservant, HiC-Pro

Oh, I see.

At the moment it's running fine... but will take that into consideration for the future if I run into any memory issues.

Thanks again, Nicolas! :)

Cheers,

Juan

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