Hello XianJun The error noted in the oryLat1 README has been fixed in oryLat2. chrUn has been eliminated in oryLat2 and thus this also eliminates the mapping problem to which you refer.
Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Xianjun Dong wrote: > HI, Jennifer > > Thanks for reply. > > I can see it's the same problem as we once discussed in UCSC mailist. > (ref. topic: "question about contig/scaffold and chrUn, again") > > Actually I have worked on the mapping problem (between chrUn and > contig/scaffold/ultracontig) for medaka. The script was tested working. > The principle is to use the contig as the basic linker to bridge UCSC > chrUn coordinate and the ultracontig/scaffold coordinate used in > original assembly (which is also used in Ensembl). If the issue is still > regarding the mapping, I'd like to be involved in the discussion. > > Otherwise, what's the difference between oryLat1 and oryLat2 in UCSC? > > Regards, > > Xianjun > > Jennifer Jackson wrote: > >> Hi Xianjun , >> >> Recently, the medaka genome was updated to a newer version. The data >> track you mention has not been through our QA release process yet, but >> when it is released we will send you an email. >> >> Meanwhile, you can access both the previous release oryLat1 and the >> new release oryLat2 on our test server. Both are annotated, but be >> aware that some of these annotation tracks have not gone through QA >> yet (or may never go through QA). >> http://genome-test.cse.ucsc.edu/ >> >> We removed oryLat1 from the main browser because of some data >> problems. We documented the problem in the oryLat1 downloads README file: >> http://hgwdev.cse.ucsc.edu/goldenPath/oryLat1/bigZips/ >> >>> ERROR NOTE: We have determined that UCSC's assembly of the chrUn >>> sequence for oryLat1 is incorrect: the gap relationships between >>> contigs within their ultracontigs are broken. We are in the process >>> of correcting this error, and plan to post a corrected data set in >>> late July. We apologize for the inconvenience. >>> >> We hope this helps to clear things up, >> UCSC Genome Bioinformatics Group >> >> Jennifer Jackson >> >> >> >>> Xianjun Dong Xianjun.Dong at bccs.uib.no >>> Mon Feb 2 02:24:32 PST 2009 >>> >>> Hi, >>> >>> There was "Human Proteins Mapped by Chained tBLASTn" track in medaka >>> genome, but it's not there now. I am wandering if it's because of the >>> wrong data or you missed to put there. It is a quite often used >>> track, at least for the incompletely annotated medaka genome. >>> >>> Regards, >>> >>> Xianjun >>> >>> >>> >>> > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
