How to convert a HG19 Hi-C hic file to HG38?

[Ian D]

Hi,

Firstly apologies as I have previously posted this message on Biostars (https://www.biostars.org/p/9479224/), which is getting views, but no answers.  I am hoping this forum is more specific to my question :)

I have a Hi-C hic file associated with the HG19 genome. How can I convert it to HG38?

I have looked at Juicer Tools dump, but it looks as though you can only extract data to a sparse format for individual, or pairs of, chromosomes.

Ideally I want to be able to extract the data to a non-binary format, convert it to HG38 (possibly via crossover), then recreate the hic file.

Has anyone done this?

Thank you.

Ian

[Neva Durand]

The best solution is to restart the juicer pipeline from scratch on the fastqs and align to hg38. 

If you have access to the merged nodups file, you can perform liftOver on the positions and use that file with Pre to create a new hic file. 

Another possibility is to use straw or juicer tools dump to extract contact matrices at all of the chromosome-chromosome pairs at the highest binned resolution (I would extract with NONE as the norm), use liftOver on the bin boundaries, and make a new hic file with the short-with-score format. I suspect this will be a little weird to be honest. Something slightly better would be to take the counts in a bin and choose randomly distributed positions within that bin and liftOver those; and even more scientifically sound would be to base that distribution on your RE and chromatin accessibility. 

Some documentation:

https://github.com/aidenlab/juicer/wiki/Pre

https://github.com/aidenlab/straw

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[Ian D]

Dear Neva,

Many thanks for the very fast reply!   What I am getting is that unless one has access to the original fastq files it is by no means a simple task to liftOver.  I only have access to the hic file deposited on GEO, but you never know the fastq may be available.  I'll look into the alternative.

[Neva Durand]

GEO should have the fastqs. They will be stored as sra files. 

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/fa7e97d3-15fc-433f-ab56-2f75115a2921n%40googlegroups.com.

[Ian D]

Thank you.  I found the SRA files after being prompted my your last reply.  That route sounds much simpler :)

If you use Biostars feel free to reply there, otherwise i'll put a summary of how I solved it.