Generating linear plots with genomealign files

[DustinSokolowski]

Hello!
Thank you for the wonderful browser. I have three quick questions about the linear plots if you don't mind.

1. Is it possible to upload a genome align file and make a linear plot as a local track? "Categorical" gives the alignment blocks but I was hoping to be able to generate the linear plots.
2. Have you had any issues generating the linear plots on the genome browser? I have tried loading a genomeAlign file I made last year (it used to load fine from the same URL) but it seems to be stuck loading for hours. I have tried multiple days this week. It's also why I'm interested in the "local" option.
3. I updated my species' assembly and I am now trying to generate a new genomecov file. The split axt file looks completely fine, however, I have been unable to convert the split axt file into a genomecov file. It works for the first 65,000/2,000,00 entires then it crashes, seemingly unable to find the Y chromosome on mm10. Have you seen this error before? I'm happy to send the split.axt file if that would help.

python3 axt2align.py mHetGlaV3.chr.sizes mm10_to_mHetGla.split1.axt mm10_to_mHetGla1.align
Traceback (most recent call last):
File "axt2align.py", line 35, in
c=chrsize[lst[4]]
KeyError: 'chrY'

Pulling the lines from the axt.split file that have "chy" as the mmus region, I don't see anything unusual.

Thank you!
Dustin

[xzhuo]

Thanks for trying our browser! Once you have the genome-align track file ready, you can load them from the local. Regarding your error, do you have "chrY" in the mHetGlaV3.chr.sizes file?

[DustinSokolowski]

Hey!

You are correct, I had the previous iteration of the .sizes fie (oops) and the genomealign file looks great now.

In terms of the local upload, I do not see a track file type that matches the genomealign format under the "1. Choose track file type:" dropdown. I've tried some of the generic bed/categorical version, but rather than making those beautiful linear plots, I end up with a bed file annotated aligned regions:

This being said, the only option to generate those beautiful linear plots seems to be in add remote track > track type > genomealign. Here's an example from when I did this a couple years ago (I didn't have issues loading the data from our lap FTP then).

I tried uploading the track as it's own datahub though it seems to be stuck on the upload screen. Perhaps something is wrong with my json?

{
"filename": "mm10_to_mHetGla.genomealign.gz",
"type": "genomealign",
"name": "mm10 to mHetGla",
"metadata": {
"genome": "mm10"
}
}

It's been here for 20 mins or so.

[xzhuo]

I'm glad you can generate the track file with no problem now. As to the local hubs, seems there is a problem. I mostly use remote tracks myself and did not catch it. @lidaof, what is the local hub json configuration of genomealign file? I can't get it working, either. If there is a bug how hard is it to fix it?

[DustinSokolowski]

I'm glad to hear it's not just me. I'd be happy using a remote track, however I'm not sure if my lab's FTP is supported on WashU. It seems like the browser tries to connect to the FTP indefinitely. I worked about a year ago but I've been having now luck since.

If you want to try for yourself, the file is here: http://wilsonlab.org/public/NMR_maternal_assembly/mm10_to_mHetGla.genomealign.gz

If it is the FTP but you have a suggestion of another place to host the file that you know should connect, then please let me know. I've tried my own drive as well but again no luck (which makes sense given permissions on the drive)

[lidaof]

Hi @DustinSokolowski , your web server is configured correctly, the reason why you cannot load it is your files are hosted on an HTTP site, in that case, you would need to use our HTTP URL (http://epigenomegateway.wustl.edu/browser/), not the HTTPS URL.
This is a JavaScript security setting, HTTPS sites cannot access contents in an HTTP site.
I will look into the local hub things, looks like we need to enable that feature as well.

[DustinSokolowski]

Hey!

Looks like the HTTP URL did the trick. Thank you for all of your patience and looking forward to the local update.

Best,
Dustin

[DustinSokolowski]

Hello @lidaof,

I'm sorry to reopen the same issue again but our groups FTP updated and it seems like we're having the same issue as earlier. I tried mixing and matching the http/https URL and we had no luck. In both instances it's stuck on this "infinite loading loop"

I'm sorry if I'm missing something simple again. Alternatively, did you get around to adding the genomecov file to the local track options?

on HTTP:

on HTTPS

[lidaof]

Hi @DustinSokolowski , no worries, sorry for get back to you late. My gut feeling is your web server is somewhat slow...would you mind send me the url(s) of your files?

I am testing the local genome align track files option, should be applied to public site soon.

[DustinSokolowski]

Sent, thank you!

[PhrenoVermouth]

Thanks for the issue, now I know that genome align files could be loaded in the remote track menu. Looking forward to the local version!