From: Mason Meyer <mmeyer20@uncc.edu>
To: Pioger, Leo <leo.pioger@igmm.cnrs.fr>
Date: Fri, May 19, 2017 at 4:35 PM
Subject: Re: All Refgene variants not displayed

Hello Leo,

My name is Mason Meyer, Support Specialist for IGB. Thank you for taking the time to contact us with your question. You asked why the default RefGene track in IGB does not display all of the gene variants seen in the UCSC refgene track for the mm9 genome. This is an excellent question and I don't know the answer off the top of my head. Please allow me to run this by our other team members to see if they know the answer to this.

Dr. Loraine or Ivory, do you know why this may be? I found a place in the mm9 genome where this is occurring (see screenshot). Do either of you have any idea why this is happening?

Thanks again,

Mason Meyer
IGB Support Specialist

From: Mason Meyer <mmeyer20@uncc.edu>
To: Pioger, Leo <leo.pioger@igmm.cnrs.fr>
Date: Tue, May 30, 2017 at 2:08 PM
Subject: Re: All Refgene variants not displayed

Hello again Leo,

After discussing your issue with the rest of the team, we think that the reason for the default RefGene track in IGB not displaying all of the gene variants seen in the UCSC RefGene track is because the default mm9 genome in IGB may be out of date compared to UCSC's data. We have created a story in our issue-tracking system so that we can update the mm9 genome in the near future. Thanks for bringing this to our attention, as we want IGB to contain the most up-to-date information. This should be updated soon, but in the meantime, please let us know if you have anymore feedback for our team.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Pioger, Leo <leo.pioger@igmm.cnrs.fr>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Wed, Jun 14, 2017 at 12:26 PM
Subject: Re: All Refgene variants not displayed

Hello,

Thanks a lot for taking time to review this issue ! Well if you want another feedback i do have another one: since i use IGB, i can't open an .svg file generated by IGB (windows nor linux-based) with illustrator (CC 2017) nor GIMP, but inkscape can open it, save it at as a simple .svg file, which can then be opened with Illustrator.

When the RefGene's IGB track will be updated on your side, will the update be automatically downloaded in our servers.

Thank you again for your time, have a great day.

Leo Pioger

From: Mason Meyer <mmeyer20@uncc.edu>
To: Pioger, Leo <leo.pioger@igmm.cnrs.fr>
Date: Sat, Jun 17, 2017 at 2:59 PM
Subject: Re: All Refgene variants not displayed

Hello again Leo,

Thanks for the additional feedback on the SVG issue you are experiencing. This is actually an issue we have known about for some time and at one point we changed the SVG Export library we are using in hopes of fixing the problem, but this resulted in more problematic behavior, so we decided to continue using our original SVG Export library. With that being said, we still wish to find an elegant solution to this issue and will be continuing to look into ways to fix the problem mentioned in the near future. This issue should be addressed in a future IGB version. I apologize for any frustration you may experience with that feature in the meantime, but please continue to update your version of IGB whenever a new version is available because this may resolve the issue for you if we are able to find a fix.

As for your question about the RefGene track, the answer is yes. Once we are able to update the Refgene track on our side, this should be updated on your side as well, as long as you are not keeping IGB running continuously without exiting the program, which I imagine you are not. If you continue to experience any additional issues with this in the future, please feel free to reach out to me so I can give you a status update on this. Once again, thank you for your patience and your feedback. If you have anything else for me, please don't hesitate to contact me.

Thanks again,

Mason Meyer
IGB Support Specialist