From: Mason Meyer <mmeyer20@uncc.edu>
To: Maureen Donlin <donlinmj@slu.edu>
CC: Ann Loraine <Ann.Loraine@uncc.edu>; David Norris <dcnorris@uncc.edu>
Date: Mon, Oct 3, 2016 at 11:31 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Hello Maureen,

My name is Mason Meyer, IGB Support Specialist. Thank you for contacting us so that we may help resolve the issue you are having with IGB.

I wanted to let you know that I am currently taking a look into your issue and I also wondered if you would mind re-sending me your GFF3 file so that I can use it for testing as I did not see it attached to the initial support request, for some reason.

If you can send me the file for testing, I believe it may help in finding a quicker solution to your issue. I look forward to hearing back from you soon.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Maureen Donlin <donlinmj@slu.edu>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Mon, Oct 3, 2016 at 11:32 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Dear Mason,

Thanks for the quick response. I've attached my GFF file which I'm using.

Regards,
Maureen
–
Maureen J. Donlin, Ph.D.

Director, Bioinformatics and Computational Biology Program
Research Associate Professor
Biochemistry & Molecular Biology
Saint Louis University School of Medicine

Doisy Research Center
1100 South Grand Blvd.
Office 611/Lab 663
314-977-8858

From: Mason Meyer <mmeyer20@uncc.edu>
To: Maureen Donlin <donlinmj@slu.edu>
Date: Mon, Oct 3, 2016 at 11:37 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Thanks Maureen,

I will give you a status update on your issue as soon as I understand more about the problem.

Thanks again,

Mason Meyer

From: Mason Meyer <mmeyer20@uncc.edu>
To: Maureen Donlin <donlinmj@slu.edu>
Date: Mon, Oct 10, 2016 at 11:08 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Hello again Maureen,

I apologize for the delay in getting back to you. I have tested the issue you are experiencing with labeling your GFF3 file and I was able to reproduce the problem. As you explained, labeling by the "ID" field in IGB causes the GFF3's "Name" field to appear as a label instead and after looking through the other labeling options I see that there is not a way to label by the GFF3's actual "ID" field.

I have not been able to find a good workaround that will allow you to label by the proper "ID" field at this time so I have sent an e-mail to our lead developer in the hopes that he may be able to help think of a solution.

There is one thing I know of that will work, but unfortunately it isn't a very elegant solution. You could edit the GFF3 file in a text editor and replace the entries for the "Name" field with your desired text (the entries from the "ID" field). I have included a screenshot of my result using this method so you can see that it will work. This would be nearly impossible to do for the entire file though, but if you wished to change the labels for just a few genes this way it may help if your goal is to export an image for a publication or something similar. On the other hand, if you need to label all of the genes by the proper "ID" field then this solution is not efficient.

Please let me know if I can assist with the workaround mentioned above or if you have any other questions. In the meantime, I will wait to hear from our lead developer and will let you know what he says. He normally gives very quick responses so I should be able to give you a status update soon. By the way, thank you very much for bringing this to our attention because I believe this is an important issue that our team will need to fix as soon as possible.

Sincerely,

Mason Meyer
IGB Support Specialist

From: Maureen Donlin <donlinmj@slu.edu>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Mon, Oct 10, 2016 at 11:12 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Mason,

Thanks for the response. I had figured out that perhaps editing the GFF3 file would get around this problem. I haven't done it yet, but it shouldn't be that difficult.

Regards,
Maureen

From: Mason Meyer <mmeyer20@uncc.edu>
To: Maureen Donlin <donlinmj@slu.edu>
Date: Mon, Oct 17, 2016 at 9:58 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Hello again Maureen,

I wanted to briefly follow up with you to see if you were able to edit your GFF3 file so that you could read your desired labels in IGB. I reached out to our lead engineer and he told me that there is no way to label by the "ID" field as seen in the GFF3 at this moment and that it would require a change to the code, so I have created a story in our issue-tracking system so we will be sure to revisit the GFF3 labeling in the near future.

I also checked to see if a GTF file may be a better option for you, as you asked in your initial e-mail. I believe you are correct in your assumption, as I seem to be able to label by the "ID" field (transcript id field in the GTF file, which is why the letters "TO" appear after the ID). I have attached a screenshot for your convenience and have also attached a GTF file in case you do not have one handy.

Please let me know if this helps resolve the issue for you or if I can do anything else to assist.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Maureen Donlin <donlinmj@slu.edu>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Mon, Oct 17, 2016 at 10:04 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Dear Mason,

Thanks for following up and for the GTF file. I was able to edit the GFF3 file to swap the ID= and Name= fields so that it now displays the systematic gene name. I appreciate your responsiveness to this issue.

Regards,
Maureen

From: Mason Meyer <mmeyer20@uncc.edu>
To: Maureen Donlin <donlinmj@slu.edu>
Date: Mon, Oct 17, 2016 at 10:11 AM
Subject: Re: GFF3 file displays Name= in place of ID=

Dear Maureen,

I am glad to hear that editing the GFF3 file worked for you. Once again, thank you for bringing the GFF3 labeling issue to our attention. Hopefully, we will be able to revisit that very soon and correct any issues there. If you ever have any more feedback for our team, please don't hesitate to contact us.

Sincerely,

Mason Meyer
IGB Support Specialist