hgRenderTracks not showing ENCODE data

[Vince Forgetta]

Hi,

When I try to render the following URL:

http://genome.ucsc.edu/cgi-bin/hgRenderTracks?clade=mammal&db=hg19&org=Human&hideTracks=1&trackHubs=&position=chr21:21846544-22346544&wgEncodeBroadHistone=hide&wgEncodeBroadHmm=hide&wgEncodeReg=show&wgEncodeRegMarkH3k4me1=dense&wgEncodeRegMarkH3k4me3=dense&wgEncodeRegTfbsClusteredV2=dense&wgEncodeSydhHistone=hide&wgEncodeUwHistone=hide&refGene=pack

I note that the cartDump reports wgEncodeReg=hide even though I set this to
"show" in the URL.

When I set this manually to "show", by changing hgRenderTracks to hgTracks and toggle the pulldown menu in Regulation to "show", then compare a cartDump to that from the above URL the only difference is the following tag/values:

_ 1474930967808
wgEncodeReg show

Adding the _=1474930967808 tag/value to hgRenderTracks URL did not solve the issue.

So, how can I get hgRenderTracks to show wgEncodeReg?

​Thanks,

Vince​

[Christopher Lee]

Hi Vince,

Thank you for your question about hgRenderTracks. You have discovered a bug in the hideTracks parameter. Unfortunately setting hideTracks=1 and then turning on subTracks of a Super Track is not working as expected.

The current workaround is to create a base session with everything hidden, and then turning on individual tracks. Here is an example URL:
http://genome.ucsc.edu/cgi-bin/hgRenderTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.hide&position=chr21:21846544-22346544&wgEncodeBroadHistone=hide&wgEncodeBroadHmm=hide&wgEncodeReg=show&wgEncodeRegMarkH3k4me1=dense&wgEncodeRegMarkH3k4me3=dense&wgEncodeRegTfbsClusteredV2=dense&wgEncodeSydhHistone=hide&wgEncodeUwHistone=hide&refGene=pack

I have made a ticket to track this bug, and we will contact you when it is fixed. Thank you for uncovering this bug!

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[Christopher Lee]

Hi Vince,

Thanks again for reporting this issue, we have fixed the hideTracks parameter and your hgRenderTracks links should work correctly now.

Let us know if you have any further questions!

Thanks,

Christopher Lee
UCSC Genomics Institute