How can I add pre-loaded bed file (if I do not have the index and just .bed file)?

[KHBHH]

Hi,

I am trying to include pre-loaded data in .bed format, and when I put the type as "categorical", it does not work, giving error that it is looking for the index. I also tried to put the type as "text" and did not work. How can I have this kind of data pre-loaded in public datahub, what type should it be?

I have included this data in the json file as but I do not know what type should I assign to it?

{ "type": "?", "url": "https://xxxxxxxxxxxx.cloudfront.net/CPG.bed", }

Thank you, I appreciate your help!

[lidaof]

HI @KHBHH in your case mentioned, the type is bed, please refer to the documentation: https://eg.readthedocs.io

[KHBHH]

Hi @lidaof ,

thank you for your reply. I have read your documentation, one bed file I am using is (.bed.gz) with its index (.bed.gz.tbi) and when I put the type="bed", it works. But I have another bed file that it does not have this format but is just (.bed). Whenever I put the type of this file to be type:"bed", it does not work. It tell me the following:

register.js:30 Worker caught an error: Error: HTTP 403 fetching https://d3ni442lubv0v0.cloudfront.net/CPG.bed.tbi

I believe it is looking for its index file, right?

This is how I have the file in my json when I try to upload a remote datahub.

[lidaof]

Hi @KHBHH if you visit the url you sent it says access denied

[KHBHH]

Hi @lidaof , yes because I do not have that file. My question is: if I only have a bed file in the following format (.bed) withiout (.gz and .gz.tbi), how can I include it in the remote datahub?

[lidaof]

Hi @KHBHH you can put the .tbi in the same folder with the .gz file, no need to specify in datahub for .tbi

[KHBHH]

Hi @lidaof, thank you!

[KHBHH]

Hi @lidaof,

So my question is a bit different, I do not have .gz with the index .tbi file. I only have .bed file format such as: https://xxxxxxxxxx.cloudfront.net/CPG.bed and when I assign the type of this file "bed" in the remote datahub json file, it does not work. Meanwhile I am able to upload this file data from (local text track) individually.

My question is that how can I include (.bed) in remote datahub json file, without having the bed file in .gz and .tbi format?

[lidaof]

Hi @KHBHH bed file in remote URL need to be compressed to bgzip and with an index .tbi file, sometimes bed file are pretty big, the browser cannot load the entire bed file into ram, that will freeze the page and brings low performance. Small bed file can be submitted for visualization with the local text feature, please see https://eg.readthedocs.io/en/latest/text.html