Hi, I'd like to visualize *.hic files (juicer) in your browser. When I add a custom track by URL to the ftp serving my file, nothing happens. I also tested the example *hic file and get the same result. Is this feature working?

Uploading files from a server:

Hi!

I would like to upload several files from an in house server to create custom tracks but every time I get the same error: 'Something about this track is broken. Please check your input.'

I don't know where the error may be because I don' have any problem uploading these files in UCSC.

Thanks for your help!

Best,

Laia

Hello

I wanted to insert in WashU fragmented tunicate genomes.

Some of them can have more than 50.000 scaffolds and display such genomes was not possible in the browser ('download infinite')
To resolve my problem I have inserted an index on scaffoldInfo table.


Christelle


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Hi,

I am trying to load multiple interaction tracks via .txt files. However, some of the txt files failed to load ( see attached screenshot). There isn't any difference in format of the files that did load successfully and those that did not. Can you advise ?


Photo

Hi,
If I want to view a binned contact matrix/ interaction matrix from an HiC experiment, what file formats can I use as inputs? Is it a valid option using the Long-range(text file format) that you have defined in the wiki?
That is e.g:
chr1,1000000,1050000 chr1,1000000,1050000 34
chr1,1000000,1050000 chr1,1050000,1100000 27
chr1,1000000,1050000 chr1,1100000,1150000 12
....
etc

All help is greatly appreciated.

Hi Daofeng,

with a set my bedgraphs that I have saved with a link, I get after a few times, when all had worked very well, suddenly an error message "Unreadable response from server, Json syntax error, Crashed upon ajaxX". Is there a way to refresh the link or something that can clear this error ? Thank you Roland

Dear Dao

For your information :
I tried to insert a custom tunicate genome in WashU but I had many errors linked to scaffold name "Invalid scaffold sequence name: R2951, Invalid scaffold sequence name: R2951 ...."

To solve my problem, I changed the type of 'defaultScaffold' column in 'config' table (makeDb.sql)
create table config (
......
defaultScaffold text not null, -> defaultScaffold longtext not null,
.....
);

My custom genome is a fragmented genome with a high number of scaffolds.

Cheers

Christelle




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If we generate new bzgip-ed and tabix-indexed bed.gz and bed.gz.tbi files and copy them in place of old versions of the same files, the embedded WashU browser and subtleKnife binary do not seem to refresh the local cached tbi file. As a result, the track then looks blank (see attached image).

Right-clicking the track and selecting "Refresh cache" does not refresh the tbi file stored in the "t" (trash?) folder of a local WashU browser installation. As a workaround, manually copying the tbi file in place on the file system seemed to help.

We're using v42.3 of the WashU browser build from source via Github (https://github.com/epgg/eg).

Photo

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We setup a web server hosted on the Jetstream server for our science gateway. On the result page, we make a link to navigate users to check the WashU Genome Browser with the data stored in the host server. The data can not be loaded directly via HTTP or HTTPS. So the browser needs to download all data loaded by the PHP script via HTTPS protocol. For some unknown reasons, the browser often can not load all tracks successfully. Here is an example:


http://epigenomegateway.wustl.edu/browser/?datahub=https://dreg.dnasequence.org/gbrowser/KcWaXdWai5yc15Wat9VclN3byd2L1gjN1MzNzkDNx0WYlJHdzRXZq9lbv9FdzVGdvQ3Ylp2byBFdsVXYmVGRvADMwITeop3dvoQKk5WYyR3ctgyZpd1ZpJkCnl2VnlmYuMXdsB3XxV2cvJ3ZvUDO2UzM3MTO0ETbhVmc0NHdlp2Xu92X0NXZ09CdjVmavJHU0xWdhZWZE9CMwAjM5hme39iCpQmbhJHdztCKnl2VnlmQK8SN4YTNzczM5QTMtFWZyR3c0Vmaf52bfR3clR3L0NWZq9mcQRHb1FmZlR0LwADMykHa6d3L&genome=hg19

I guess the reason is the response speed of web server. Do you think so?

Because we use the hosting service, so we can not improve too much about the server response. Do you think we have any options to change the timeout for the genome browser?



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Dear browser users,
Welcome to try our version 43 browser. In this version we improved the HiC track display and added yeast genome upon request. Thank you.

http://wiki.wubrowse.org/V43:_improved_rendering_of_HiC_tracks_and_yeast_genome_added
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