From: Nick Schurch <nickschurch@gmail.com>
To: Ann Loraine <Ann.Loraine@uncc.edu>
Date: Thu, Mar 23, 2017 at 9:33 AM
Subject: IGB chromosome synonyms...

Hi David, Ann,

I'm having a problem with chromosome synonyms not loading correctly in IGB 9.0.0 on Max OS Sierra (I'm at home so I can't easily check other OS's I'm afraid).

My chromosome.txt file looks like:

chrC Chloroplast Pt ChrC C

chrM Mitochondrion Mt ChrM M

My data use Pt in both bigwigs and bamfiles.

When I load the quickload server and try to load data for the chrC chromosome, nothing appears. Instead, a new 'Pt' chromosome appears int he chromosome listings. This I can load data for but, obviously, the problem is that this chromosome doesn't have any annotations for it so its of limited utility.

There is no error in the console log to suggest that IGB is struggling with this chromosome.txt file, and I checked that it uses tabs. It does have a blank line at the end, but that shouldn't be a problem right?

This was working on previous version of IGB - as you can see I emailed you back in 2015 about a similar problem but figures out the solution and had it working. I've not changed the files since then so has IGB changed the way it deals with these files recently?

Thanks,

Nick

On Tue, 8 Sep 2015 at 12:00 Nick Schurch <nickschurch@gmail.com> wrote:

Hi David,

Sorry to bother you with this but I'm having an issue with making chromosome synonyms work for a quickload server.

I have a quickload server with a chromosome.txt file that looks like:

Chloroplast chrC Pt ChrC C
Mitochondrion chrM M ChrM M

When I load up the genome chrC shows up (A thaliana, 2009). The data int he quickload use Pt. My understanding is that the chromosome.txtx file should mean that pt data are trated as chrC, but when I load the data I get a Pt chromosome appearing, which obviously has no annotations listed.

Am I doing something wrong with the chromosome file?

I'm using v8.4.3 in linux or 8.4.2 in windows and see the same thing.

–
Cheers,

Nick Schurch