How to manually edit .hic file metadata?

[Michael Johnston]

Hi,

I have multiple .hic files that were aligned to hg38 using the attached hg38_limited.chrom.sizes file.

I edited the filename at some point, so now I have certain files that used "hg38.chrom.sizes" while others used "hg38_limited.chrom.sizes", but the contents of this chrom.sizes file was the same in both cases.

Now, I cannot load both files in to Juicebox simultaneously (one as "observed" and one as "control") because they have "different genomes".

Is there a way for me to edit the metadata in the .hic file so that the genomeId fields in the hic file headers match?

I have been looking that the .hic file format specifications and I cannot figure out how to read / edit these files.

The closest I can get is the following, from the supplemental of Durand and Shamim et al 2016.

The code for reading and writing the hic file format is available at the Juicebox GitHub repository; consult the class DatasetReaderV2 in package juicebox.data for reading and the class Preprocessor in package juicebox.tools.utils.original for writing.

But then I cannot find these files or the documentation surrounding them.

Please advise. Thank you!

- Michael 

 

[Neva Durand]

Hello,

I'm sorry but there's no way to edit this because changing the metadata changes the file pointers.  You could obviously recreate the hic file, using "hg38" as the genome ID (the hg38.chrom.sizes will get translated to this).  Also in general you can just use hg38 instead of the chrom.sizes file.

Sorry about that, we are looking into changes to the file format to make this more flexible.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org