Release 6 Drosophila melanogaster genome?
Nelson Lau
Hello,
Do you have an ETA when the newest Release 6 of the Drosophila Melanogaster genome will be loaded into the UCSC Browser? The current latest build is Dm3, Release 5.
Thanks,
Nelson Lau, Ph.D.
Assistant Professor - Biology
Brandeis University
415 South St, MS029
Science Receiving
Waltham MA 02454, USA
Ph: 781-736-2445
http://www.bio.brandeis.edu/laulab
Matthew Speir
Thank you for your question about updating the D. melanogaster assembly in the UCSC Genome Browser. A preview of the BDGP Release 6/dm6 Genome Browser is available on our preview site at http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=dm6. However, please keep in mind that this our test server, and that much of the data has not undergone our standard quality review process and is subject to change. We do have plans to release this to our public website at http://genome.ucsc.edu/, but I do not have a projected date of when that might happen.
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
--
Nelson Lau
Thanks, Matthew. Is the Liftover tool able to help us convert the Dm3/Release5 coordinates to the Dm6/Release6 coordinates? We have a paper accepted where the work was done on Dm3, but the journal would prefer all the coordinates be adjusted to Dm6, including BED files. I understand this build is on the test server, but presumably the new build will be released soon? Please advise how we can convert all our file coordinates to Dm6.
Matthew Speir
Yes, you can use the liftOver tool just like you normally would to convert dm3 to dm6 coordinates. You can access the web interface for liftOver on our preview site at http://genome-preview.ucsc.edu/cgi-bin/hgLiftOver. To convert the coordinates from dm3 to dm6 use the following settings:
Original Genome: D. melanogaster
Original Assembly: BDGP R5
New Genome: D. melanogaster
New Assembly: BDGP Release 6 + ISO1 MT
If you want to use the command line liftOver utility, you can find the liftOver chain file on our preview downloads server here: http://hgdownload-test.soe.ucsc.edu/goldenPath/dm3/liftOver/dm3ToDm6.over.chain.gz. Again, please keep in mind that the data on our preview servers has yet to undergo our standard quality assurance process and may be subject to change.
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