From: <Loraine>, Ann <Ann.Loraine@uncc.edu>
Date: Monday, November 24, 2014 at 8:52 AM
To: "Dingwall, Andrew" <Adingwall@luc.edu>
Cc: "Meyer, Mason" <mmeyer20@uncc.edu>, "Freese, Nowlan" <nfreese@uncc.edu>
Subject: Re: IGB update on Drosophila version 6 annotations and genome

Thanks for getting back to me so quickly!

Yes, you probably will need to view the old ChIP-Seq data using the older version. If your older data are BAM, bedgraph or wig files, then they probably reference the older version - dm5. You could probably open your files in the new version, but the alignments will map to the wrong place if the genome has changed a lot - e.g., some parts added or removed.

Probably the best thing would be to re-align your data onto the new version and re-run your old pipeline on it. Depending on when you did your original analysis, you may be pleasantly surprised — much of the software we use for this has improved a LOT in the past few months! You may get better results and the software will like be faster and easier to run.

In my lab, we are using bowtie to align reads and macs2 to find and score peaks. And we’ve started using DiffBind (from Bioconductor) to identify differentially bound peaks across samples.

Also, we'd be happy to help you set up an IGB QuickLoad site you could use to publish/share your data sets. Nowlan Freese and Ivory Blakely (cc’d on this email) can walk you through it, and documentation is here: https://wiki.transvar.org/confluence/display/igbman/Creating+QuickLoad+Sites

Very best wishes,

Ann Loraine

From: <Dingwall>, Andrew <Adingwall@luc.edu>
Date: Monday, November 24, 2014 at 8:25 AM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: RE: IGB update on Drosophila version 6 annotations and genome

Hi Ann,

Thanks for letting me know! I have some new RNAseq data that was annotated using v6, so I'll try it on the new IGB fly genome. I still have most of my ChIP-seq data annotated using the older version. I was told that the two versions are quite different and the older ChIPseq data must still be viewed using the older version. Is this the case?

Have a great Thanksgiving!

Andrew

Andrew K. Dingwall, PhD
Oncology Research Institute, Gene Regulation and Epigenetics Program
Departments of Pathology and Microbiology & Immunology
Stritch School of Medicine
Loyola University Chicago
2160 S. First Avenue
Cardinal Bernardin Cancer Center, Rm. 334
Maywood, IL 60153
(708) 327-3141; fax (708) 327-3342
adingwall@luc.edu
http://dingwall-lab.weebly.com

Sent: Sunday, November 23, 2014 at 12:51 PM
From: Loraine, Ann <Ann.Loraine@uncc.edu>
To: Adingwall@luc.edu <Adingwall@luc.edu>
CC: Meyer, Mason <mmeyer20@uncc.edu>; Freese, Nowlan <nfreese@uncc.edu>

Hello,

Back in June you wrote asking about whether (and when) the IGB team would update the Drosophila genome in IGB to the latest version - version 6, released July 2014.

I just wanted to let you know that we’ve posted the new fruit fly genome in the IGBQuickLoad.org site. I’m sorry for the long wait!

Now, if you start IGB and click the fruit fly image on the start screen, you will go directly to the July 2014 (version 6) release of the D. melanogaster genome. Also, the latest gene models from Flybase will load automatically.

However, you can still access the older genome version using the menus in the Current Sequence tab (on right of IGB window.)

We have not yet thoroughly tested the new genome sequence and annotations in IGB and will be doing that in the coming weeks. In the meantime, if you notice any problems, I’d be grateful if you would let us know.

Once we’ve completed testing, we’d like to make an announcement to the Drosophila research community. If you could recommend a forum where we could reach many people, we'd appreciate the pointer!

Best wishes,

Ann Loraine
Associate Professor
UNC Charlotte
Dept. of Bioinformatics and Genomics
http://bioviz.org
http://lorainelab.org

From: Dale Dorsett <dorsettd@slu.edu>
Date: Tuesday, August 12, 2014 at 1:02 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: Re: your call about fruit fly data

Hi Ann,

Thanks for looking into this!

In addition to release 6, there are many folks who would be interested in the last of the release 5 annotations, since essentially all of the deposited modENCODE data was done with release 5. My lab has also generated over 30 genomic ChIP, GRO-seq and RNA-seq type of experiments using release 5, but find that when we look at the data in IGB that many of the annotated mRNAs are way out of date. I have been dealing with this in my unsophisticated way by parsing the flybase genome rel5.56 gff file to make “gene” and “mRNA” and “ncRNA” bed files to load into IGB. Eventually I will have to liftover the coordinates on our data files to release 6, but the last version of release 5 would also be really helpful.

Thanks again,

-Dale

Dale Dorsett, PhD
Professor
Biochemistry and Molecular Biology
Saint Louis University School of Medicine
1100 South Grand Boulevard
Saint Louis, MO 63104

Office: 314-977-9218

*In response to a call from: Dale Dorsett, PhD

From: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Date: Tuesday, August 12, 2014 12:17 PM
To: Dale Dorsett <dorsettd@slu.edu>
CC: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: your call about fruit fly data

Hello,

Sorry I missed your call about the fruit fly genome annotations and IGB.

A couple of other people have asked about this.

I just took a look at the FlyBase Web site.

It looks like they released Dmel R6 on July 16 along with annotation files.

We should be able to update the fruit fly data for IGB fairly quickly.

Thanks for getting in touch and we hope to get back to you soon with good news about the update.

Best wishes,

Ann Loraine

From: Ann Loraine <aloraine@uncc.edu>
Date: Monday, June 23, 2014 at 1:43 PM
To: "Dingwall, Andrew" <Adingwall@luc.edu>
Subject: Re: current genome annotations

Hi,

I just took a look at the FlyBase Web site.

It looks like they are preparing to release an all-new genome assembly (v6) this summer. Going along with this new assembly release, they’ll also release the version 5.57 genome annotations re-mapped onto the new assembly.

Currently, IGB is showing the April 2006 genome assembly, also called “dm3” and “BDGP Release 5.” From what I can tell, it looks like the April 2006 version is the latest available but will be superseded when the version 6 assembly comes out.

When you visit fruit fly in IGB, a track of annotations labeled “RefGene” automatically load into the viewer. These were taken from the UCSC Genome Informatics Table Browser - they correspond to alignments of RefSeq mRNA records onto the assembly that were done by the UCSC team.

It sounds like it would be far more useful if IGB instead provided access to the FlyBase gene model annotations, which probably people in the field regard as the “canonical” gene models annotations. Does that sound right?

I looked through the FlyBase site and found a GFFv3 file that looks like it has everything I would need to set this up. Mainly I would just need to reformat the file and add some meta-data to it…such as functional annotations.

Also, I wanted to mention that IGB now has a Galaxy integration feature you might find useful. If you have a BAM or BED file in Galaxy, you can click on its name and a link labeled “View in IGB” will appear. The previous link did not work, but we fixed it recently. I’ve been using this feature a lot lately to look at results from various tools available in Galaxy that I didn’t have time (or patience to install on my local computer. Seems like for smaller genomes like fruit fly or Arabidopsis, Galaxy is an especially nice tool because the files we work with are not too large.

Let me know if you have further suggestions about the fruit fly gene models and assembly! I’ll keep you posted on the progress.

Ann