WashU Epigenome Browser Visualization

[John He]

Hi,

I was wondering how to format one of the Hi-C datasets for visualization as interacting loops on the WashU browser like it has been done for GM12878 dataset.  Is this done by reformatting a HiCCUPS looplist output file or am I mixing up two different things?  Thank you for your time.

Best,

John 

[Neva Durand]

Hi John,

I'm not 100% sure what you're referring to - could you send a screenshot or tell me how you loaded it?

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Daofeng Li]

Hi John,

This is Daofeng from WashU browser group. For now, our public browser http://epigenomegateway.wustl.edu/browser/ support HiC tracks in tabix format, which is described at http://wiki.wubrowse.org/Long-range

Thanks to the help from Muhammad from Aiden lab, we are now supporting the .hic format used by Juicebox as well at our test browser (http://epgg-test.wustl.edu/browser/), documentation can be found at http://wiki.wubrowse.org/HiC. There are still functions under development and we are planning to release this feature in next release of WashU browser in near future.

Thanks and please let me know if you encounter any issue.

Best,
Daofeng

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From: "John He" <john.z...@gmail.com>
To: "3D Genomics" <3d-ge...@googlegroups.com>
Sent: Sunday, July 10, 2016 6:51:01 AM
Subject: WashU Epigenome Browser Visualization

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[Andrew]

Hi Daofeng,

Could you provide an update on utilizing hic files on the Epigenome Browser?

I've tried to add a custom hic file, but I am getting the error 'Tracks need to be hosted on a web server that is accessible by this browser server.'. I'm pretty sure my file is publically available as I am hosting it on a public webserver.

Do you also have a sample hosted hic file that I could use to test to see if it works?

Thanks!

Andrew

[Andrew]

Hi Daofeng,

Yes - I do see the example on the hg19 browser and it looks good. I now realize the notice about accessible webservers is always present and not the problem I am having. 

When I try my own hic file on mm10 genome (works well in juicebox), I get "NO DATA IN VIEW RANGE" at all scales. It seems like it's not recognized. Not sure how to troubleshoot aside from asking if all juicer-generated hic files have been working on the browser for you.

Thanks for the time,

Andrew

On Mon, Nov 28, 2016 at 10:31 AM, Daofeng Li <dl...@wustl.edu> wrote:

Hi Andrew,

If you go to custom tracks panel, you could see the Hi-C button for submitting the track

You click the ‘Use example’ button can see an example HiC track.

Let me know if this helps or not. Thanks a lot.

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[Andrew]

Daofeng,

I've tried both with and without the 'chr', option. My chrom.sizes does have chr, so that is what I tried first.

I've also played with other options, but it doesn't seem to work.

Andrew

On Mon, Nov 28, 2016 at 11:40 AM, Daofeng Li <dl...@wustl.edu> wrote:

Hi Andrew,

could you please try tick the ‘chromosome has chr’ option?

sorry for that which is not quite clear to see.

On Nov 28, 2016, at 1:37 PM, Andrew <andd...@gmail.com> wrote:

Hi Daofeng,

Yes - I do see the example on the hg19 browser and it looks good. I now realize the notice about accessible webservers is always present and not the problem I am having. 

When I try my own hic file on mm10 genome (works well in juicebox), I get "NO DATA IN VIEW RANGE" at all scales. It seems like it's not recognized. Not sure how to troubleshoot aside from asking if all juicer-generated hic files have been working on the browser for you.

Thanks for the time,

Andrew

On Mon, Nov 28, 2016 at 10:31 AM, Daofeng Li <dl...@wustl.edu> wrote:

Hi Andrew,

If you go to custom tracks panel, you could see the Hi-C button for submitting the track

You click the ‘Use example’ button can see an example HiC track.

Let me know if this helps or not. Thanks a lot.

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[Muhammad Saad Shamim]

Hey Guys,

The file actually has to be seekable (e.g. Dropbox url hosting does not work, but Box does).

One quick way to test if the webserver is properly configured is to open the url for the file in Juicebox.

Go to Juicebox>File>Open>From URL (aidenlab.org/juicebox)

If the url works in Juicebox, then the issue is somewhere on the WashU Browser's end.

But if it doesn't open in Juicebox, then the hosting server is not properly configured.

​Can you let us know whether the urls work with Juicebox?

​Best,​

- Muhammad Saad Shamim

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[Andrew]

Yes, the seekable is a good point and testing it with Juicebox is a good test. In this case the files open fine with Juicebox.

We are currently testing to see where from the WashU browser side things may be going wrong.

Andrew

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[Muhammad Shamim]

Just a quick update on this thread.

Error was related to IGV version, which has been updated and new jars will be pushed out soon.

[Neva Durand]

Hello everyone,

The error that caused this has been resolved; we have pushed a new IGV jar and one small update to the GitHub.  Thanks to Andrew and Daofeng for debugging.

Best

Neva

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