Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
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Environment:
IGB 6.7 (trunk) but also affects 6.6
Description
As always, feel free to re-assign this as needed.
In the trunk version of IGB the Affy probe sets are not displayed correctly.
To repeat:
1. choose A_thaliana_Jun_2009
2. zoom in on a gene region
3. choose data set IGB (DAS2)>affy>ATH1-121501
note there probe sets data sets for mouse, human, etc
you don't have to use A thaliana
4. load data
What's happening is that the probe sets are somehow getting put into a different track.
What you should see is the attached, a screen capture from IGB 6.5.3, following setting the label field to "id."
(I am showing the id in the image so that you can more easily find this probe set again if you need to.)
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
Did this happened again?
There is still a bug/some 'weirdness' with these files. When you check mark them to get them into the data management table, the show up with 2 track checked. If I uncheck 2 track before loading, they still load up as 2 track, with the two track box suddenly rechecked. Then I uncheck and it makes 1 track. However, the pink probes are NOT properly offset to the top/bottom indicating 'side'. They completely overlap the cyan glyph. I have to activate 2 track again and then uncheck it to get them to show the offset.
If the track is permitted to load as two track and then made 1 track, it loads and displays fine.
However, both human and plant are properly loading a 'single' track for each probe file.
Done in r9540.
Please test it with other probeset files too.
Multi track issue
The pink bars are the probes. These are getting read from the link.psl file. Note that IGB translates probe-to-target coordinates into genomic coordinates using the genometry data models.
Passed V.13601, Mac, Java 1.06.0_37
Tested with A. thaliana and H. sapiens. Probes appear in pink, offset from the read but in the same track, as depicted in last two photos attached to this bug.