Reporter has been informed Chlorocebus sabaeus has been added to IGB.

From: Ann Loraine <Ann.Loraine@uncc.edu>
Date: Sun, Sep 9, 2018 at 2:24 AM
Subject: Re: New reference genome
To: Mason Meyer <mmeyer20@uncc.edu>, Ivory Blakley <ieclabau@uncc.edu>
Cc: Osama Youssef <osama.youssef@hsc.utah.edu>

Hello Ivory & Mason,

Osama (cc'd, and see below) would like us to add green monkey (Chlorocebus sabaeus) to IGB Quickload.

Let's try to do this next week.

We should get the sequence data (as usual) from UCSC but get the reference gene models from the GFF available from NCBI as he mentioned below. It would be more convenient to get the gene models from UCSC as usual, but I don't see them listed in the table browser. I think what may have happened is that NCBI has annotated the genome but UCSC has not yet imported the annotations into their database.

Talk with you Monday!

Ann

From: Osama Youssef <osama.youssef@hsc.utah.edu>
Date: Tue, Sep 4, 2018 at 11:15 AM
Subject: Re: New reference genome
To: Mason Meyer <mmeyer20@uncc.edu>

Hi Mason,

Yes please create a request to add the Chlorocebus sabaeus genome to IGB Qickload.

Thanks,

Osama

From: Mason Meyer <mmeyer20@uncc.edu>
Date: Fri, Aug 31, 2018 at 6:54 PM
Subject: Re: New reference genome
To: Osama Youssef <osama.youssef@hsc.utah.edu>
Cc: "Loraine, Ann" <Ann.Loraine@uncc.edu>

Hello again Osama,

Thanks for your response. I downloaded your mentioned files and spent time testing to see if I could find a workaround that would allow you to view your files of interest in IGB without having to upload them every time, but it seems there is currently not a way to do this for custom genomes.

If you would like, I can create a request in our issue-tracking system to add the Chlorocebus sabaeus genome to our IGB Quickload site so that you and other IGB users will be able to select this genome from the list of available genomes. Does this sound like it would work for your case? If so, let me know and I will create the request so our team can plan to add this genome to IGB in the near future. I look forward to hearing back on this when you are able.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Osama Youssef <osama.youssef@hsc.utah.edu>
Date: Tue, Aug 28, 2018 at 6:59 PM
Subject: Re: New reference genome
To: UNCC <mmeyer20@uncc.edu>

Thanks Mason for your follow up.
I downloaded the chromosome fasta files from this link https://www.ncbi.nlm.nih.gov/genome/?term=txid60711[orgn]
I combined the fasta files into one file and opened it on IGB from "open genome file"
Then I downloaded the gene annotation file (GTF) for Chlorocebus sabaeus from this link https://uswest.ensembl.org/info/data/ftp/index.html
I just dragged this GTF file to IGB to display the genes
I cannot figure out how I can keep the genome fasta file and GTF file on IGB without the need to upload them every time I open IGB.
Please let me know what do you think?

Thanks for your help!
Osama

From: UNCC <mmeyer20@uncc.edu>
Date: Tue, Aug 28, 2018 at 6:18 AM
Subject: Re: New reference genome
To: osama.youssef@hsc.utah.edu
Cc: Ann.Loraine@uncc.edu

Hello Osama,

My name is Mason Meyer, IGB Support Specialist. Thanks for your patience on this issue. I understand you are trying to load the Chlorocebus sabaeus, or Green Monkey, genome, is this correct? I am happy to help with this!

Do you have a reference genome file you can share with me? If the file is too large, I can track down a reference genome for us.

Also, I am wondering what steps you were taking to try and load the reference genome. If you let me know the steps you took, I can advise you on the process. You should be able to load your reference genome into IGB by dragging the file onto the IGB window as soon as IGB starts up (before selecting a genome). This will load your reference genome as a track in IGB and you can press Load Data/Sequence to view the individual base pairs.

Please let me know if you are able to load the reference genome by dragging the file onto the IGB window. If not, I will continue looking into this to see why the genome is not loading properly. In this case, I will need a reference genome file to use for testing. If you are able to share your file, please do so. Otherwise, I will track down one myself. I look forward to hearing back on this when you have the chance. Thanks again, Osama!

Thanks,

Mason Meyer
IGB Support Specialist

From: Ann Loraine <Ann.Loraine@uncc.edu>
Date: Thu, Aug 23, 2018 at 2:39 PM
Subject: Fwd: New reference genome
To: Mason Meyer <mmeyer20@uncc.edu>, osama.youssef@hsc.utah.edu

Hello,

It is nice to hear from you.

I am forwarding your message to Mason Meyer, our user support specialist. He will get back to you with an answer, and possibly some additional questions about the genome you mentioned.

Thank you for using IGB,

Ann Loraine