correction, test server is: http://genome-test.cse.ucsc.edu/
-Galt On Thu, 6 Aug 2009, Galt Barber wrote: > > I just finished chainSelf on danRer6. > You can see it on hgwdev-test. > > -Galt > > > On Fri, 24 Jul 2009, Xianjun Dong wrote: > >> Hi, Galt, >> >> Thanks so much for the work. >> >> Are you saying the contigs unmapped to chromosome (like Zv8_NA***, or >> Zv8_scaffold***)? I am not sure how this will make the display 'noisy'. For >> study like duplicated genes, I guess it's OK to leave them out; I just >> checked the Ensembl genes in Zv8 -- only a small fraction (~5%, 1579 out of >> total 27855 Ensembl genes) are in contig Zv8_***. I am not sure if other >> people have special need for that. But principally, they should be there, >> since they are part of the genome assembly, anyway. Maybe the better way is >> to treat it as how you did for a normal species pair: including both chain >> and net. (see below) >> >> I found that the selfChain idea is very interesting/useful in several ways, >> for example, in re-constructing the evolution history of Whole-genome >> Duplication (WGD, e.g. 2R WGD for human, 3R WGD for teleost fish), in >> comparing the paralog genes within one species, especially when it's hard to >> find a suitable genome as out-group. One question is, if there is only chain, >> it might be still hard to know which alignment blocks (the unit in chain) are >> from the same locus before duplication. Actually, I expected there are >> something like 'joined Chain'. I know the net data is somehow a sorted chain. >> The higher-scoring non-overlapping chains are always put more top. This >> brainchild can help people to 'filter out' the low-scoring chain (for >> example, those by repeat or wrongly assembling, and finally are put into >> unmapped contigs). So, I will be really appreciated if you can make the >> selfNet. >> >> BTW, I suggest you can move the selfChain (and selfNet, if so) to the >> Comparative Genomics. Now they are in "Variation and Repeats". Maybe you >> have some reason for that. >> >> Thanks again >> >> >> Xianjun >> >> >> >> Galt Barber wrote: >>> >>> Hi! I am working on self-chain for Zv8 now. >>> I had a question about whether people want >>> to include the approx. 11,000 contigs >>> in the self-chain, or leave them out. >>> It's more work to leave them out, >>> but it may make the display easier to >>> read. On the other hand, perhaps having >>> the scaffolds included is important to >>> you for some reason. >>> >>> Which way would be better for your work? >>> >>> thanks >>> >>> -Galt >>> >>> >>> On Wed, 27 May 2009, 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, >>>>>> >>>>>> >>>> >>>> -- >>>> Sterding (Xianjun) Dong >>>> PhD student, Boris Lenhard's group >>>> Bergen Center of Computational Science >>>> Bergen University, Norway >>>> Mobile: 0047-47361688 >>>> Telephone: 0047-55584022 >>>> Skype: xianjun.dong >>>> >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >> >> -- >> ========================================== >> Xianjun Dong >> PhD student, Lenhard group >> Computational Biology Unit >> Bergen Center for Computational Science >> University of Bergen >> Hoyteknologisenteret, Thormohlensgate 55 >> N-5008 Bergen, Norway >> E-mail: [email protected] >> Tel.: +47 555 84022 >> Fax : +47 555 84295 >> ========================================== >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
