Cannot upload data to the IGV Web app

[cgrunau]

Dear IGV team We have data available in https://zenodo.org/record/7113924 of which we would like to share the visualisation via https://igv.org/app/

I tried it out with Dropbox a while ago and it worked, but stopped working a couple of days ago. I uploaded data to Zenodo https://zenodo.org/record/7113924

Still not working

Java-Script console reads: Failed to load resource: Origin https://igv.org is not allowed by Access-Control-Allow-Origin. Status code: 200

The combination Zenodo + IGV webapp would actually be great. Is there anything we/you can do?

Many thanks Christoph

[jrobinso]

I don't know anything about Zenodo, but Dropbox is working fine for me. Can you open this shared URL?

https://tinyurl.com/2ezc2yvx

[jrobinso]

BTW, a subtle but important distinction -- nothing is uploaded to igv.org/app. It is in fact downloaded to your computer that is running the application (igv-webapp) that itself is downloaded from igv.org/app.

Data server requirements are documented here: https://github.com/igvteam/igv.js/wiki/Data-Server-Requirements. Dropbox meets these requirements, Zenodo does not appear to be setup for this type of use case.

[cgrunau]

Thank you. Actually https://tinyurl.com/2ezc2yvx is not working at my work place:

[jrobinso]

That's rather strange. Is it possible your organization is using a proxy that strips headers from http response headers, or that dropbox access is blocked? You can investigate this with Chrome "developer tools", or similar tools on other browsers. To do this first open developer tools in a tab on your browser from the View menu (View > Developer > Developer tools). Then paste the tiny url in your address bar and go. After the page loads click the network tab. Scroll to the file affected and clicked "Headers" on the tab to the left (see screenshot below). Under response headers you should find the header access-control-allow-origin: *. Let us know what you find.

[cgrunau]

Thank you. The files don't load at all. I found in the XHRs for the dropbox served files: "Failed to load resource: The certificate for this server is invalid. You might be connecting to a server that is pretending to be "dl.dropboxusercontent.com", which could put your confidential information at risk." Definitely a restriction of our university firewall since I can connect over the cell phone. Nevertheless maybe an issue.

[jrobinso]

I would suggest raising this issue with your IT department.

[Oksanak22]

Hello! I try to use the https://igv.org/app/. My data is a big sorted.bam file and i have converted itt into .bedpe with

module load bedtools bedtools bamtobed -i sorted.bam -bedpe > sorted.bedpe But when I uploaded I don't see anything
Could anyone help me with that? Thank you,

[jrobinso]

A couple of questions. (1) how did you load it, as a file with the file browser or as a url? (2) what genome assembly are you using, and have you checked the chromosome names in the bedpe to be sure they match the chromosome names in the genome assembly you have selected?

If you can share the file or a few lines of it I will look at it.

Also, BTW, the igv webapp runs on the browser on your computer, nothing is uploaded.

[Oksanak22]

1. I have loaded it as a local file ( first option from the second tab)
2. I used a mapping to a reference genome When I opened the .bedpe file and it looks like . -1 -1 . -1 -1 23f81c3e-a413-4404-a2f8-cd63c45ab211:49999:53887 0 . .

[jrobinso]

That does not look like a valid bedpe file, you can do a web search for bedpe format but the first 6 columns should contain chromosome name, start, end, second chromosome name, start, end.

[jrobinso]

Looking at bedtools documentation I found this when using the bedpe option

Lastly, when an end is unmapped, the chromosome and strand will be set to “.” and the start and end coordinates will be set to -1. By default, this is disabled and the output will be reported in BED format.

If all your lines are like this it would explain why you don't see anything.

[Oksanak22]

Thank you, @jrobinso for your advices. I see I have to check the mapping process. Аlthough I used bwa bwasw -b 4 -q 1 -r 200 -T 10 -z 55 to map reads to the genome.

[Oksanak22]

Hello, Could you guide me @jrobinso on how to get the proper .bedpe file? I converted bed file to .bedpe with bedtools with the bamtobed function.

[jrobinso]

@Oksanak22 Sorry, no, I don't have any experience with those tools.