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lidaof / eg-react

WashU Epigenome Browser
https://epigenomegateway.wustl.edu
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Unable to run VR mode #153

Closed deniseomahony01 closed 4 years ago

deniseomahony01 commented 4 years ago

I have been trying to visualize Chromatin interactions on the Epigenome browser for a region of interest, however as soon as I select 'VR mode' in Settings the browser freezes and then the page crushes. Can you explain why this happens and whether I can do anything to fix it?

lidaof commented 4 years ago

Sorry for that @deniseomahony01 , I am working on trying to fix this issue.

lidaof commented 4 years ago

Hi @deniseomahony01 , can you try refresh to 50.4.0, it should be fixed...sorry for the delay

image

deniseomahony01 commented 4 years ago

Dear Li, I am really sorry for the delayed reply. I tried running the VR mode again from different computers and servers and it gives me an error message: 'Access this site over HTTPS to enter VR mode'. Is it possible that this is a bug?

Thank you. Denise

On Thu, 27 Feb 2020, 23:05 Daofeng Li, notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 , can you try refresh to 50.4.0, it should be fixed...sorry for the delay

[image: image] https://user-images.githubusercontent.com/102806/75486668-90e08b00-5972-11ea-9011-00af43eec08b.png

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lidaof commented 4 years ago

Hi @deniseomahony01 no worries.

This is normal, you can go to our https site to avoid this warning: https://epigenomegateway.wustl.edu/browser/

deniseomahony01 commented 4 years ago

Dear Li, Thank you for your assistance I have managed to access the VR mode on the browser. May I ask you another question? I have carried out an analysis (Chicago package - Bioconductor) that generates a text file containing all available chromatin interactions in specific regions of the genome. I would like to visualize these interactions on the browser in VR mode. How can I do this?

Kind Regards, Denise

On Thu, 5 Mar 2020 at 22:48, Daofeng Li notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 no worries.

This is normal, you can go to our https site to avoid this warning: https://epigenomegateway.wustl.edu/browser/

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lidaof commented 4 years ago

Hi @deniseomahony01 you are welcome.

Good point, I will try add this function. Thanks for suggestion.

deniseomahony01 commented 4 years ago

Dear Li, The reason why I am asking is because according to the authors of the paper 'Chromatin interactome mapping at 139 independent breast cancer risk signals' and according to the package vignette which I have attached below (pdf and photo), the output files generated by running the R Package ('Chicago' package of Bioconductor) can be uploaded on the Washu epigenome browser for interaction visualization.

[image: image.png]

Thank you for your time, Kind Regards,

Denise O' Mahony

On Fri, 6 Mar 2020 at 17:18, Daofeng Li notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 you are welcome.

Good point, I will try add this function. Thanks for suggestion.

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lidaof commented 4 years ago

Hi @deniseomahony01 sorry for the long delay, I finally managed to get it working for longrange track with help from @smhsu . here is a screenshot it works for one the longrange track in our public hub. let me know if it works for you.

image

deniseomahony01 commented 4 years ago

Dear Li, Where can I upload my own text file (containing chromatin interactions) in order to visualize the interactions?

Kind Regards, Denise O' Mahony

On Fri, 13 Mar 2020 at 17:22, Daofeng Li notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 sorry for the long delay, I finally managed to get it working for longrange track with help from @smhsu https://github.com/smhsu . here is a screenshot it works for one the longrange track in our public hub. let me know if it works for you.

[image: image] https://user-images.githubusercontent.com/102806/76634885-8dbdd100-6514-11ea-84cf-db7af8bf4198.png

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lidaof commented 4 years ago

Hi @deniseomahony01 you can use text format: https://eg.readthedocs.io/en/latest/text.html#longrange or compressed and index with tabix: https://eg.readthedocs.io/en/latest/text.html#longrange both text and gzip'ed track file(s) can be uploaded from your own computer.

deniseomahony01 commented 4 years ago

Dear Li, I am really sorry to bother you once again but I haven't managed to do this yet. So I have this long range text file with all the possible interactions for the region of interest and i went to Tracks > Text tracks > Selected long range text format> uploaded my file > selected VR mode. But this is what I get: [image: image.png] Am I doing something wrong? Thank you for your help and once again I am sorry that I bothered you so many times.

Kind Regards, Denise

On Mon, 16 Mar 2020 at 16:31, Daofeng Li notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 you can use text format: https://eg.readthedocs.io/en/latest/text.html#longrange or compressed and index with tabix: https://eg.readthedocs.io/en/latest/text.html#longrange both text and gzip'ed track file(s) can be uploaded from your own computer.

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lidaof commented 4 years ago

Hi @deniseomahony01 can you re-upload the image? also can you send me your text file directly for me to test?

thank you!

deniseomahony01 commented 4 years ago

Dear Li, find below the image and the long-range text file. Also, the region i am interested in is at the SNP rs17356907 at position chr12:96027756-96027761. Thanks.

On Sun, 22 Mar 2020 at 23:39, Daofeng Li notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 can you re-upload the image? also can you send me your text file directly for me to test?

thank you!

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lidaof commented 4 years ago

Hi @deniseomahony01 I am able to view your text file in the long range track format, I guess the data is too sparse to be viewed in VR mode. I will try to adjust the parameter see if I could get it working. (please note the columns need be separated by Tabs in your text file)

lidaof commented 4 years ago

Hi @deniseomahony01 I spent more hours on this issue...but could not figured it out why. Can you try your full dataset see if you can view it in VR mode?

deniseomahony01 commented 4 years ago

Thank you for trying, I will try my full data and let you know. You also said you were able to view my data in the long range track format. Did you do this by uploading the long range text file I sent you in the 'view local tracks' or the 'text tracks' option?

On Mon, 23 Mar 2020 at 21:00, Daofeng Li notifications@github.com wrote:

Hi @deniseomahony01 https://github.com/deniseomahony01 I spent more hours on this issue...but could not figured it out why. Can you try your full dataset see if you can view it in VR mode?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lidaof/eg-react/issues/153#issuecomment-602794549, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOUSZBIA6LHCS2W5DCAB2PDRI6WTTANCNFSM4K2ILABA .

lidaof commented 4 years ago

text tracks option. local track means the track still formatted accordingly (tabix+bgzip) but exists in local drive, text track means the track is a plain text file.

yes, i was able to view your example data pasted here.

lidaof commented 4 years ago

closing for now, feel free to reopen it or open a new issue.