HiC data not in .hic format

[Sharp, Sandra]

I have two questions.  If you are not the right place for the answers, please point me in the right direction, if you can.

1.  I have been viewing mouse muscle .hic data on the UCSC browser with great success. Additional HiC data for non-muscle tissue is available in GEO that I would like to look at for comparative, but it is not in hic format.  

Here are two example links for processed data (albeit zipped) for a HiC sample from embryonic stem cells followed by the description of how the data were processed.  Is there an easy way to make these data available for the UCSC browser, or would I have to take the raw data and use the Aiden lab pipeline.

https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2533nnn/GSM2533818/suppl/GSM2533818%5Fgc%5Fes1.tar.gz

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM2533818&format=file&file=GSM2533818%5Fgc%5Fes1%2Etar%2Egz

Data processing

Library strategy: HiC Hi-C data was processed using the Cwalks pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=690). In brief, raw sequencing reads were mapped independently to the mm10 reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded. supplementary_files_format_and_content:Each processed file represent pairwise information of the observed genome contacts and can be further analyzed using the "Shaman" pipeline (https://bitbucket.org/tanaylab/shaman). assembly: mm10

FYI - both the links in the above paragraph gave error messages!

2.    My second question is, is there a way to take the results of 4 HiC embryonic stem cell runs, numbered in the above project 1-4, and combine the data in order to achieve a finer resolution.  (Perhaps I should be writing to the paper authors about this.)

Thank you so much for your continuing help!

Sandy Sharp

Sandra B. Sharp, PhD

Professor Emerita, Biological Sciences

Cal State LA

[Matthew Speir]

Hi, Sandra.

Thank you for your question about viewing HiC data in the UCSC Genome Browser.

Additional HiC data for non-muscle tissue is available in GEO that I would like to look at for comparative, but it is not in hic format.

The data needs to be in .hic format to view it in the browser. The Aiden lab's Juicer pipeline or HiCExplorer available from Galaxy would be good places to start.

We also offer the "interact" format which can draw arcs between different genomic locations, but doesn't offer any of the other functionality of the hic format: https://genome.ucsc.edu/goldenPath/help/interact.html.

My second question is, is there a way to take the results of 4 HiC embryonic stem cell runs, numbered in the above project 1-4, and combine the data in order to achieve a finer resolution. (Perhaps I should be writing to the paper authors about this.)

Yes, we would definitely recommend reaching out to the paper authors for guidance on combining multiple runs of HiC data. 

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Genome Browser, User Support

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[Sharp, Sandra]

Dear UCSC Browser Team:

I am following up on the email below, specifically the section that is copied right here:

Me:  Additional HiC data for non-muscle tissue is available in GEO that I would like to look at for comparative, but it is not in hic format.

UCSC:  The data needs to be in .hic format to view it in the browser. The Aiden lab's Juicer pipeline or HiCExplorer available from Galaxy would be good places to start.

I have been working through the HiCExplorer hands on tutorial.  If I understand correctly, the end file will be .h5.  I can't find any method to change a file from .h5 to .hic to use on the UCSC Browser.  Can you clarify.   (I am also posting this question on the Galaxy Community.)

Thank you!

Sandy Sharp

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From: Matthew Speir <msp...@ucsc.edu>
Sent: Saturday, April 20, 2024 2:33 PM
To: Sharp, Sandra <ssh...@exchange.calstatela.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] HiC data not in .hic format

 

[Sharp, Sandra]

I think I may have found something.  I found a page by searching the HiC tools for converting cool to hic.   The word cool shows up in the files that I have been accumulating during a Exploring HiC handson tutorial.   I am going to explore that as soon as I get a chance.  

Sandy Sharp

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From: Sharp, Sandra <ssh...@exchange.calstatela.edu>
Sent: Sunday, June 30, 2024 6:26 PM
To: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>