From: Ann Loraine <Ann.Loraine@uncc.edu>
To: Nick Schurch <nickschurch@gmail.com>
CC: Mason Meyer <mmeyer20@uncc.edu>
Date: Thu, Mar 23, 2017 at 9:38 AM
Subject: Re: IGB chromosome synonyms...

Hi Nick,

It is good to hear from you!

I'm wondering if there could be an interaction with the genome.txt file for this genome?

I'm emailing Mason - he will look into it and get back to you with questions - probably today or the next few days.

All the best,

Ann

From: Mason Meyer <mmeyer20@uncc.edu>
To: Nick Schurch <nickschurch@gmail.com>
CC: Ann Loraine <Ann.Loraine@uncc.edu>
Date: Thu, Mar 23, 2017 at 12:49 PM
Subject: Re: IGB chromosome synonyms...

Hello Nick,

I hope you've been doing well. I'm sorry to hear you are experiencing difficulties with IGB. Hopefully, we will be able to find a quick solution to the problem. I can spend some time testing the IGB Synonyms system, but it may help if you can share your Chromosome.txt file with me. I see the screenshot you've sent, but sometimes I've noticed minor details, such as extra tab characters, that cause unexpected behavior. If you can share this, please do, but if you can't, please let me know and I will attempt to reproduce the issue without it.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Nick Schurch <nickschurch@gmail.com>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Fri, Mar 24, 2017 at 9:00 AM
Subject: Re: IGB chromosome synonyms...

Sure, here it is. https://uod.box.com/s/csglqcpd8gdlihuua37up5g43jhkc5fm

From: Mason Meyer <mmeyer20@uncc.edu>
To: Nick Schurch <nickschurch@gmail.com>
Date: Tue, Apr 4, 2017 at 8:37 PM
Subject: Re: IGB chromosome synonyms..

Hello again Nick,

I apologize for the delay in getting back to you about your issue. I have spent several hours looking into this and am easily able to reproduce the issue, but I have not yet found a solution to the problem. I understand that this is a frustrating issue and it is important that we find a quick solution. I have tried several things to fix the problem, thinking that maybe there was something very minor about the chromosome.txt causing a problem, but now I am starting to think as you did; that there may be a bug in the synonyms system.

I am going to spend more time looking into this to see when this issue starting appearing in IGB. I will most likely end up creating a story for this in our issue-tracking system so that we can plan to fix it in the near future, but I am interested in your workaround from 2015, as well. Do you happen to remember how you were able to resolve the issue in 2015, as you mentioned? It seems like the issue from 2015 is the exact same as the one you are having now, and I can confirm that the synonyms system was recently working, so this behavior is very puzzling to me. I will continue to investigate to determine how severe the problem is, but in the meantime, if you have any info about your workaround from 2015, I would love to hear it. Also, thank you very much for bringing this issue to our attention!

Sincerely,

Mason Meyer
IGB Support Specialist

From: Mason Meyer <mmeyer20@uncc.edu>
To: Nick Schurch <nickschurch@gmail.com>
Date: Thu, Apr 20, 2017 at 9:16 PM
Subject: Re: IGB chromosome synonyms..

Hello again Nick,

I hope you've been doing well. I've continued to look into your issue with the chromosomes.txt file and I have to admit that during my initial round of testing, a crucial step to adding the chromosome.txt in IGB slipped my mind, and I wondered if you might have done the same thing, by chance.

At the bottom of the Data Sources tab in IGB Preferences, there is a Personal Synonyms area where you can add your chromosome synonym file (see screenshot). I wanted to quickly run this by you because I was successfully able to merge ChrC and chromosome Pt using your chromosomes.txt file (see other screenshot).

Please let me know if this solution is able to resolve the problem you have been experiencing. If not, our team will continue to work to find a solution.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Nick Schurch <nickschurch@gmail.com>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Fri, Apr 21, 2017 at 5:32 AM
Subject: Re: IGB chromosome synonyms..

Hi Mason,

I haven't tried that actually. I shouldn't have to do this if the chromosomes.txt file is served by the quickload server though, right? It seems that the problem we're having is that the chromosome.txt file somehow isn't being picked even though its valid...

From: Mason Meyer <mmeyer20@uncc.edu>
To: Nick Schurch <nickschurch@gmail.com>
Date: Mon, Apr 24, 2017 at 10:44 AM
Subject: Re: IGB chromosome synonyms..

Hello again Nick,

Sorry for the delay in getting back to you. I wanted to run this question by the rest of the IGB team to ensure that I am not saying something that's not true, but yes, you are correct. You should not need to add the chromosomes.txt file under the Data Sources tab, as I may have thought. As you've said, it seems like the file just isn't being picked up even though its definitely valid. This is something we will want to fix as soon as possible, but I am curious to know if adding the chromosome.txt file under Data Sources can be used as a temporary workaround for you so that you can see the data tracks on the same chromosome. I know this method is not ideal if the Quickload is being used from several different computers, but it may be able to help you in the short term.

Thank you very much for bringing such a serious issue to our attention. If you have anymore feedback for me, please let me know. I imagine that we will work to fix this issue very soon and then I will be sure to contact you to see if you would want to check out the new fix before our next release.

Thanks again,

Mason Meyer