Track hub debugging

[matte...@dbmr.unibe.ch]

Hi,

I am trying to charge a track hub but it always pop up an error:

ERROR: Couldn't open https://data.cyverse.org/dav-anon/iplant/home/matteozoia/analyses/ATACseq/genomes.txt

Nevertheless, the genome.txt format and location it is correct. Why could be the issue??

Best regards

Zoia Matteo, Ph.D. Student 

Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory 

Department for BioMedical Research (DBMR) 
University of Bern 
G812, Murtenstrasse 35 
CH - 3008 Bern 
SWITZERLAND

[Luis Nassar]

Hello, Zoia.

Thank you for your interest in the Genome Browser.

We believe this could be a sharing issue on the CyVerse end, if we go up the directory structure:

https://data.cyverse.org/dav-anon/iplant/home/matteozoia/analyses/

We do not see any of the lower directories as being there, the genomes.txt is a 404. We only see a single file:

https://data.cyverse.org/dav-anon/iplant/home/matteozoia/analyses/GSE47948_RNAseq_RPKM.txt.gz/

You may have to try the CyVerse "share" portal, select all of the data/folders in CyVerse and select the Public Links option, as shown below:

After that, all the files should be available. Let us know if that works for you, or if you need further assistance.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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[matte...@dbmr.unibe.ch]

Hi Luis,

Thank you so much I will try it as soon as possible!! =)

Very helpful!!

My best regards and thanks again for your fast answer!

Best,

Matteo 

Zoia Matteo, Ph.D. Student 

Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory 

Department for BioMedical Research (DBMR) 
University of Bern 
G812, Murtenstrasse 35 
CH - 3008 Bern 
SWITZERLAND

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Da: Luis Nassar <lrna...@ucsc.edu>
Inviato: martedì, 11. maggio 2021 20:36:29
A: Zoia, Matteo (DBMR)
Cc: UCSC Genome Browser Discussion List
Oggetto: Re: [genome] Track hub debugging

 

[matte...@dbmr.unibe.ch]

Hi,

at the end it wasn't working and had to switch for a public accessible repository.

I then choose for Github but still found an error in the header. I don't understand where could be the error.

ERROR: Response is missing required header Content-Length: for url https://github.com/matteozoia4/UCSC_ATACseq/blob/main/hub.txt Couldn't open https://github.com/matteozoia4/UCSC_ATACseq/blob/main/hub.txt

Best,

Matteo 

Zoia Matteo, Ph.D. Student 

Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory 

Department for BioMedical Research (DBMR) 
University of Bern 
G812, Murtenstrasse 35 
CH - 3008 Bern 
SWITZERLAND

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Da: Luis Nassar <lrna...@ucsc.edu>
Inviato: martedì, 11. maggio 2021 20:36:29
A: Zoia, Matteo (DBMR)
Cc: UCSC Genome Browser Discussion List
Oggetto: Re: [genome] Track hub debugging

 

Hello, Zoia.

[matte...@dbmr.unibe.ch]

Hi,

Here the files I am using to create this overlay page in UCSC.

Maybe can be helpful.

Best,

Matteo 

Zoia Matteo, Ph.D. Student 

Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory 

Department for BioMedical Research (DBMR) 
University of Bern 
G812, Murtenstrasse 35 
CH - 3008 Bern 
SWITZERLAND

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Da: Zoia, Matteo (DBMR)
Inviato: mercoledì, 12. maggio 2021 09:13:46
A: Luis Nassar

[Luis Nassar]

Hello, Matteo.

It looks like the problem you were having was similar, you have to produce the proper outlink URL both from cyverse as github. You can click the Raw link on github to get the desired link:

It turns the following page (https://github.com/matteozoia4/UCSC_ATACseq/blob/main/hub.txt) into just your hosted .txt file: https://raw.githubusercontent.com/matteozoia4/UCSCATACseq/main/hub.txt

If you try to attach that hub (http://genome.ucsc.edu/cgi-bin/hgHubConnect) you will see the following error:

ERROR: Duplicate genome mm10 in stanza ending line 5 of https://raw.githubusercontent.com/matteozoia4/UCSCATACseq/main/genomes.txt 

As described, the genomes.txt file has two stanzas both with mm10 as the designated assembly (https://raw.githubusercontent.com/matteozoia4/UCSCATACseq/main/genomes.txt):

genome mm10
trackDb mm10/trackDb.txt

genome mm10
trackDb mm10/mytrackDb.txt

It seems the top one was just for testing, so you will want to change that file to just the 2nd entry:

genome mm10
trackDb mm10/mytrackDb.txt

Once you do that your hub should work properly. I have created a duplicate of your hub for testing purposes with the changes shared in this message (test hub can be found here: https://hgwdev.gi.ucsc.edu/~lrnassar/track_hubs/RM27539/hub.txt) and was successfully able to load the data. See the following link to see your ATAC-seq data on mm10:

http://genome.ucsc.edu/s/view/RM27539

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

[matte...@dbmr.unibe.ch]

Hi Luis,

thank you so much for your help!

Yes one it was a tryout indeed.

Thank you a lot for your help! It is really appreciated!

My best regards and thank you so much!

Zoia Matteo

Zoia Matteo, Ph.D. Student 

Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory 

Department for BioMedical Research (DBMR) 
University of Bern 
G812, Murtenstrasse 35 
CH - 3008 Bern 
SWITZERLAND

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Da: Luis Nassar <lrna...@ucsc.edu>
Inviato: giovedì, 13. maggio 2021 00:29:33