Thanks for the good news Personally, I might have to use zebrafish self-chain data before July. Could you kindly guide me how to do that myself? I mean the zv8, if possible.
Regards, Xianjun Donna Karolchik wrote: > hi Xianjun, > > You'll be pleased to hear that we do indeed have the zv8 assembly back > on our active project list, and hope to have it available on the > public site by perhaps sometime in July, depending on other incoming > priorities and staffing levels. We will announce the release on our > [email protected] mailing list when the browser becomes > available. > > -Donna > --------------- > Donna Karolchik > UCSC Genome Browser Project Manager > http://genome.ucsc.edu > > > Xianjun Dong wrote: >> Hi, >> >> OK. I am back with the same request now, after the >> assembly/annotation of Zv8 is done. >> >> We (and also the community, I think) know that, Zv8 was expected as a >> big improvement for Zv7, and it IS indeed, from the analysis report >> they released. So, we eagerly request UCSC, as one of the main hubs >> of data/tool for bioinformatics, to >> 1. update danRer6 (Zv8) new assembly on UCSC >> 2. make hg18:danRer6 chain/net alignment >> 3. put zebrafish self-chain alignment. >> >> Thanks >> >> Regards, >> >> Xianjun >> >> >> Jennifer Jackson wrote: >>> Hello, >>> One of our scientists has some specific ideas concerning the >>> zebrafish assembly as follows: >>> >>> They think the main reason the genome is so difficult to assemble >>> was due >>> to the DNA collection strategy:- >>> http://www.sanger.ac.uk/Projects/D_rerio/Zv3_assembly_information.shtml >>> >>> The FAQ indicates there should be a finished genome by the end of >>> this year: >>> http://www.sanger.ac.uk/Projects/D_rerio/faqs.shtml#factsnine >>> >>> Maybe you could discuss your suggestion with the sequencing project, >>> and if it would help them, we could discuss it further. >>> >>> Thank you for your offer to help improve the data, >>> Jennifer Jackson >>> UCSC Genome Bioinformatics Group >>> >>> Xianjun Dong wrote: >>>> To those who might concern, >>>> >>>> Zebrafish has been one of the most studied models in study of whole >>>> genome duplication and development, but its genome assembly is not >>>> so well (which is naturally difficult also due to the whole genome >>>> duplication there). We also noticed much duplication closely mapped >>>> in same chromosome, which actually are proved as assembly error in >>>> zv7, by BLATing in the new assembly Zv8 >>>> (http://pre.ensembl.org/Danio_rerio/Info/Index). Before Zv8 >>>> annotation get done (which might help to some extent, but not all), >>>> I am thinking if UCSC could make a self-chain for zebrafish, just >>>> like you did for human. If that information offered, we could write >>>> a script to quickly check those 'tandem' duplications close in >>>> genome, which can eventually help to improve the quality of the >>>> current assembly. >>>> >>>> If you think this might not be done in the coming soon by your >>>> plan, I will be appreciated if you can offer any assistance for me >>>> to try it myself. >>>> >>>> Regards, >>>> >>>> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
