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
