Request for help: annotation track disappears on zoom-in
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Audrey Michel
Apr 8, 2016, 12:12:01 PM4/8/16
to genome...@soe.ucsc.edu
Hi,
We have recently added the Maize genome (Zea_Mays_B73) to our mirror on http://gwips.ucc.ie. However, we have noticed that zooming in on in some chromosomal regions results in the annotations track disappearing (e.g. if you display region 1:180,710,096-180,769,963, the annotations are visible, but then disappear on zoom in to 1:180,742,955-180,744,646).
We think it may be related to #bin size for the annotation table. We use refGene table format and increase our #bin size every 2^17. However, we are not sure if this is correct.
Any advice on this issue would be appreciated.
Kind Regards,
Audrey
Brian Lee
Apr 11, 2016, 8:08:40 PM4/11/16
to Audrey Michel, genome...@soe.ucsc.edu
Dear Audrey,
Thank you for using the UCSC Genome Browser and your question about zooming issues on annotation tracks in your mirror.
I believe you are correct about the issue around bin you are seeing, but there may be quick fix by loading your table as a custom track. If you go to the Table Browser on your mirror and set your group to "Annotation Tracks" and the track to "MaizeGDB_gene" and table to "MaizeGDB_gene" you can change the output format to "custom track" and then click "get output". This will allow you to then give the data a unique name and description before clicking "get custom track in genome browser" which will then allow you to visualize your file on your mirror without the zooming issues.
You may wish to look through our archives of mailing list answers to investigate your process of loading tables, https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome-mirror/load$20table, or please do reply if you continue to have problems.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to genome...@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.
All the best,
Brian Lee
UCSC Genomics Institute
Thank you for using the UCSC Genome Browser and your question about zooming issues on annotation tracks in your mirror.
I believe you are correct about the issue around bin you are seeing, but there may be quick fix by loading your table as a custom track. If you go to the Table Browser on your mirror and set your group to "Annotation Tracks" and the track to "MaizeGDB_gene" and table to "MaizeGDB_gene" you can change the output format to "custom track" and then click "get output". This will allow you to then give the data a unique name and description before clicking "get custom track in genome browser" which will then allow you to visualize your file on your mirror without the zooming issues.
You may wish to look through our archives of mailing list answers to investigate your process of loading tables, https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome-mirror/load$20table, or please do reply if you continue to have problems.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to genome...@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.
All the best,
Brian Lee
UCSC Genomics Institute
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