Hello Xianjun, Here is a wiki page on chains and nets: http://genomewiki.ucsc.edu/index.php/Chains_Nets
You would need to download the kent source tree: http://genome.ucsc.edu/FAQ/FAQlicense.html#license3 I hope this information is helpful to you. Kayla Smith UCSC Genome Bioinformatics Group ----- "Xianjun" <[email protected]> wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
