New Ciona Genomes (ci3 and cioSav2)

[Lance Parsons]

I have started working with a lab that does research on Ciona and we
have noticed that there are two new genomes available in the "test" UCSC
genome browser. I'm right now trying to get a handle on the current
state of reference genomes and annotations and setup some standards for
the lab. I have a couple of questions about the two ciona species on UCSC:

1. Is there any known timeframe when they (ci3 and cioSav2) will be
available in the main UCSC browser? Are there things we can do to help
with that?

2. Can you tell me specifically which references will be used for Ciona
intestinalis (ci3) and Ciona savignyi (cioSav2)? Also, which gene
annotations will be loaded for these?

Thanks for any information you can provide. Having a standardized set of
tools at UCSC is very helpful and we look forward to building those up
for the ciona species.

--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

[Matthew Speir]

Hello Lance,

Thank you for your question about these Ciona genomes in the UCSC Genome
Browser.

For your first question, I believe there are plans to release the ci3
genome browser to our public site at some point in the future.
Unfortunately, I can't provide a timeframe for when this might happen.
The cioSav2 browser is likely never to be released to our public site.
This is due to an agreement with Ensembl and NCBI that requires
assemblies to be deposited in GenBank before we can add them to our
public site. It looks like Ensembl may have released a browser for this
genome, http://www.ensembl.org/Ciona_savignyi/Info/Index, but it's
likely that this was done before this agreement was in place.

For your second question, you can always look at the assembly
description page to see the source of the genome. For example, on the
ci3 assembly description page,
http://genome-test.soe.ucsc.edu/cgi-bin/hgGateway?db=ci3, you can see
links to NCBI that provide information on the assembly source:
https://www.ncbi.nlm.nih.gov/assembly/527578. The cioSav2 assembly
description page,
http://genome-test.soe.ucsc.edu/cgi-bin/hgGateway?db=cioSav2, also
contains links to the source of the genome, which is the Arend Sidow lab
at Stanford: http://mendel.stanford.edu/sidowlab/ciona.html.

For the annotations on these genomes, what is currently there is likely
to be the only annotations for these genomes that we provide. If the
researchers you are working with are generating their own annotations or
other data, and they want to share these with the community, I would
recommend that they create a track hub:
http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html. Track hubs
are collections of track data and configuration files that are placed in
a publicly-accessible web location that can then be loaded into the UCSC
Genome Browser. Additionally, we maintain a list of publicly listed
track hubs that others have created and decided to share with the UCSC
Genome Browser community: http://genome.ucsc.edu/cgi-bin/hgHubConnect.
(Ensure that you are on the "Public Hubs" tab.) If these researchers
create a track hub, we would be more than happy to add this to our list
of publicly available track hubs. When that time comes, just send a
message to our mailing list, gen...@soe.ucsc.edu, and note that you
would like to submit a public hub.

Additionally, please keep in mind that these genomes currently reside on
our test server which has software and data that can change at any time
as there are items that have yet to go through our QA process before
release to our public site.

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group