Details
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Type:
Support
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Labels:None
Description
From: Robin D Hatton <rdzialo@uab.edu>
Date: Tuesday, April 7, 2015 at 4:11 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: IGB question
Hi Ann,
I hope you received my LOS last month and that the resubmission went well.
Today I tried to use IGB v8.3.2 to analyze some old data we have from a ChiP-chip experiment where the tiled array genome was mm8. I manually loaded refGene from UCSC (DAS) but I couldn’t load the name of the genes and on some of the chromosomes (1-9) I couldn’t even see the exon/intron structure. I know it’s a pain that I have to use the old build but there’s not much I can do about it now. Do you have any ideas on how to get the genes labeled? I know on older versions of IGB this worked automatically, so should I use an older version?
Thanks,
Robin
Attachments
Issue Links
- relates to
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IGBF-536 Add MM8 Genome Annotations to IGB Quickload and make sure to include the Title and Description field
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- Closed
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Activity
From: Robin D Hatton rdzialo@uab.edu
Sent: Wednesday, April 08, 2015 11:41 AM
To: Meyer, Mason
Subject: Re: Reply to your IGB Question
Hi Mason,
Changing the label field to id resulted in the gene being labeled with NM accession number (as does changing it to “label”) not with the gene name.
See attached.
Thanks,
Robin
From: <Meyer>, Mason <mmeyer20@uncc.edu>
Date: Wednesday, April 8, 2015 at 11:05 AM
To: Robin Hatton <rdzialo@uab.edu>
Cc: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: RE: Reply to your IGB Question
Hey Robin,
Sorry for the frustration. It seems that the BED file being output by the UCSC (Das) Server does not contain the gene name field, only the NM Accession number as an identifier. Our team will need to go through the process of mapping the correct gene name to the proper accession number and will add the updated file to the IGB Quickload site for your convenience.
Ann says that we should be able to complete this task by Friday so I will be sure to contact you by the end of the week to give you a status update.
Again, I am very sorry for the recent frustration. Thanks again for your feedback!
Thanks,
Mason Meyer
From: Robin D Hatton rdzialo@uab.edu
Sent: Wed 4/8/2015 12:07 PM
To: Meyer, Mason
Subject: Re: Reply to your IGB Question
Hi Mason,
Thanks so much!
Robin
From: <Meyer>, Mason <mmeyer20@uncc.edu>
Date: Wed 4/8/2015 12:18 PM
To: Robin Hatton <rdzialo@uab.edu>
Subject: RE: Reply to your IGB Question
You’re welcome!
-Mason Meyer
From: Mason Meyer <mmeyer20@uncc.edu>
Date: Wed 4/8/2015 11:27 AM
To: Robin D Hatton <rdzialo@uab.edu>
CC: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: Reply to your IGB Question
Hello Robin,
This is Mason Meyer, the Support Specialist for the IGB team. I’m sorry to hear about your recent issue with the new version of IGB. Thank you very much for bringing this to our attention. As a result of your issue we are planning on adding the MM8 genome annotations to the IGB Quickload site sometime in the near future and we will keep you updated on our progress. This should provide a better experience for you as the genes will be labeled by default.
In the meantime, you can label the genes by first clicking on the Track Label and then going to the Annotation tab at the bottom of IGB. There is a section in this Annotation Tab called “Labels and Strand” where there is an option to select a “Label Field”. Change this to “id” to view the unique Gene id above the gene models in your selected track. If this does not resolve your issue for some reason please let me know so that we can work to find a different solution.
Also, thanks again for your LOS last month. Ann is very grateful for your support as is the rest of the IGB team. Your feedback really helps the rest of the IGB community as well so we hope that you will continue to support us and provide feedback about IGB into the future.
Thanks again,
Mason Meyer