WormBase/website — Issue #34: #135 pseudogenes on gbrowse
Author: Paul-Davis
Created: 2012-02-01 13:30:42+00:00
State: open

Todd Harris

written 2009-09-22

Changed status from new to open.
Changed responsible from webdev_team to norie.
Changed version from WS205 to WS206.

#2 Norie de la Cruz

written 2009-10-28

Changed status from open to new.
Changed responsible from norie to acabunoc.

#3 Abigail Cabunoc

written 2010-02-05

Issue #247 was marked as a duplicate of this issue.

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#4 Todd Harris

written 2010-09-17

Changed component from Classic WormBase to GBrowse.

#5 Paul Davis

written 2011-01-17

Changed version from WS206 to WS221.

Looks like this issue has re-surfaced, if it was fixed at some point since the creation of this ticket?

Which I'm guessing it must have been.

http://www.wormbase.org/db/gb2/gbrowse/c_elegans/?name=III:9012530..9017279

Paul

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Edit
#6 Todd Harris

written 2011-01-17

Changed responsible from acabunoc to norie.

Another gbrowse configuration issue.

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#7 Paul Davis

written 2011-01-26

Changed version from WS221 to WS222.

The dev site gb2 doesn't even display introns now, there is just a gap in the gene models track :(

Could this be sorted before WS222 goes live?

Cheers

Paul

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Edit
#8 Norie de la Cruz

written 2011-01-26

We've updated gb2 versions and libraries and working to update the aggregators in the config files.

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#9 Norie de la Cruz

written 2011-03-04

Changed status from new to open.

#10 Norie de la Cruz

written 2011-04-21

Changed status from open to resolved.

#11 Paul Davis

written 2011-07-20, last edited 2011-07-20

Changed status from resolved to open.

It seems like the code fixing this issue never made it out onto the live site and there still appears to be a slight issue on the dev where at least you see exons and introns.

Live issue: http://www.wormbase.org/db/gb2/gbrowse/c_elegans/?name=III%3A4638295..4640528

Gene structure appears but the introns and exons appear as block glyphs so essentially appears to be concatinated exons. Gene summary page has Nucleotides (coding/transcript) info populated - 1707/2234 bp this is misleading.

Dev issue: http://dev.wormbase.org/gb2/gbrowse/c_elegans/?name=III%3A4638295..4640528

Gene structure appears in Gbrowse but is indistinguishable from coding genes. this issue moves through to the gene summary page where Nucleotides (coding/transcript) info is populated - 1707/2234 bp

Jonathan Ewbank reported this to me when we were discussing a CDS->Pseudogene transition.

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Edit
#12 Todd Harris

written 2011-08-05

Changed responsible from norie to tharris.

These two instances are currently running the exact same config but with different data sources. Something has changed between 225/226. Will reassess once 226 is live.

Likewise with the gene page. Please check sequence coordinates on the new site since we don't have resources to go back and fix on the current. We're still working on sequence display so won't be able to check actual sequence.

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Transferred over from bitbucket.