Problem with highlight feature

7 views

Skip to first unread message

Perry, James

unread,

Apr 24, 2018, 11:28:56 AM4/24/18

to gen...@soe.ucsc.edu

Hello Genome Browser Staff,

I have been using the highlight feature to identify specific variants in the genome browser for several months. I build URLs with start-end positions and use “&highlight= … “ for each variant I want to display. This worked very nicely last February and I could display any number of variants (I never tried more than 50) over any size of genomic start-end range.

Recently, I have noticed that the URLs fail a good deal of the time. I’m using Google Chrome and the Chrome browser’s “spinner” simply stops and I am left with a blank, white screen. If I do a “view-source”, I get the unfinished HTML included at the end of this email.

Here are simple examples of two URLs - one that works and one that does not. The difference is a 10kb shift in the start-end positions.

URL that works:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr17%3A14348000-14600000&highlight=hg19.chr17%3A14490000-14490000%2300FF00%7Chg19.chr17%3A14495000-14495000%2300AA00&hgS_doOtherUser=submit&hgS_otherUserName=jim892&hgS_otherUserSessionName=OASIS_liver

URL that does not work:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr17%3A14358000-14610000&highlight=hg19.chr17%3A14490000-14490000%2300FF00%7Chg19.chr17%3A14495000-14495000%2300AA00&hgS_doOtherUser=submit&hgS_otherUserName=jim892&hgS_otherUserSessionName=OASIS_liver

The problem is somehow linked to my “otherUserSessionName”. If I click the “default tracks” button and save to a newSessionName, I can successfully use the newSessionName (try OASIS_test2 instead of OASIS_liver) with any position range. I don’t understand what the “default tracks” would be adjusting that would solve the issue. Your insight would be greatly appreciated!

Thanks in advance for your help and please let me know if I can help by providing additional information.

James A (Jim) Perry, PhD, MS

Assistant Professor, Department of Medicine

University of Maryland School of Medicine

670 W. Baltimore St., HSL-III Room 4053

Baltimore, MD 21201

=== view-source from the failed URL =====

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">

<HTML>

<HEAD>

<TITLE>Human hg19 chr17:14,358,000-14,610,000 UCSC Genome Browser v364</TITLE>

</HEAD>

=== end of view-source from failed URL =====

Jairo Navarro Gonzalez

unread,

Apr 25, 2018, 5:13:14 PM4/25/18

to Perry, James, gen...@soe.ucsc.edu

Hello James,

Thank you for using the UCSC Genome Browser and reporting your issues.

Your sessions were failing to load because of an issue with All GENCODE's 2-way Pseudogenes track. We have fixed the problem on our development site, and it will be released during our next release cycle. In the meantime, you can either append "&wgEncodeGencode2wayConsPseudoV14=hide" to your session URL to hide the V14 2-way Pseudogenes track or change the position to end at 14,605,000 instead of 14,610,000 to avoid the pseudogene item. For example, here is the fixed URL with the hidden gene track:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr17%3A14358000-14610000&highlight=hg19.chr17%3A14490000-14490000%2300FF00%7Chg19.chr17%3A14495000-14495000%2300AA00&hgS_doOtherUser=submit&hgS_otherUserName=jim892&hgS_otherUserSessionName=OASIS_liver&wgEncodeGencode2wayConsPseudoV14=hide

Thank you again for reporting this issue. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genomics Institute

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/BLUPR0301MB2003A7FF7E9107C1534F8B428C880%40BLUPR0301MB2003.namprd03.prod.outlook.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.

Reply all

Reply to author

Forward

0 new messages