About how to convert .h5 file to csv file

[Jiang Xu]

Hello guys,

   I have a question about the hic matrix file generated from hiccomparematrix. What we what to do is to list certain bins that contain the differential contact frequencies into a table. Is there a way to convert the .h5 file to csv files?

Thank you very much!

Best!

Jiang

[Vivek Bhardwaj]

Yes, you can use "HiCExport" tool to export your .h5 files into the "Ginteraction" format. It's a simple .tsv format file with region1, region2, and score, (score = interaction frequency between region 1 and 2) 

Best Wishes

Vivek

--------

Vivek Bhardwaj

Post-doc Researcher

Hubrecht Institute

3584CT Utrecht 

The Netherlands

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[Jiang Xu]

Hi Vivek,

   Thank you so much for you rapid response!

Best regards!

Jiang

Lin Chen's Research Group

Department of Biological Sciences

University of Southern California

[Jiang Xu]

Hi Vivek,

  I found that there's no HiCExport tool in the latest version of  HiCExplorer. HiCExport is only available in HiCExplorer 2.1.2. So could you tell me how to install a particular version of HiCExplorer using conda?

Thank you!

Best!

Jiang

On Thu, Sep 26, 2019 at 2:30 PM Vivek Bhardwaj <vbhard...@gmail.com> wrote:

[Vivek Bhardwaj]

Hey Jiang

The name has been changed to hicConvertFormat in the latest version. You can try that one..

Best Wishes

Vivek

--------

Vivek Bhardwaj

Post-doc Researcher

Hubrecht Institute

3584CT Utrecht 

The Netherlands

[Jiang Xu]

Hi Vivek,

 Thank you so much for you help!

Best!

Jiang