Hi David, This problem is now fixed on our test server (http://genome-test.cse.ucsc.edu), and the fix should be out on our regular site next week.
If you do take a look at the fix on genome-test, please be aware that there is a lot of untested and experimental data there. -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/05/10 12:22, Brooke Rhead wrote: > Hi David, > > I see what you are seeing now! If I first zoom in on the 5' exon, I see > the numbering starting at 66798504 for "Genomic chr1", but then just > below that, under "Side by Side Alignment", the numbering for the > genomic sequence starts at 66797793. > > This looks like a bug. I will report it to our engineers. Thank you > for pointing it out! > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > David F Barker wrote on 10/5/10 6:52 AM: >> Hi Brooke, >> >> Thanks for the reply. I'll keep that in mind and see if that's what >> I've missed, but I'm not sure that explains it, because it seems to me >> that I've seen the exact same sequences (i.e. the 5' ends of specific >> mRNAs) aligned with differently numbered genomic segments, and of >> course, the genomic numeration should not be variable. >> >> David B. >> >> >>>>> Brooke Rhead <[email protected]> 10/4/2010 9:19 PM >>> >> Hi David, >> >> The "View details of parts of alignment within browser window" link >> changes when you zoom in or out on a region in the Genome Browser. If >> >> the entire mRNA alignment fits into your Browser window, both alignment >> >> links on the RefSeq Genes page will be the same. However, if you are >> zoomed in on only part of the alignment, you will see only that part >> when you click on "View details of parts of alignment within browser >> window". >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> David F Barker wrote on 10/4/10 2:18 PM: >>> I have noticed a couple of times now that mRNA sequence genome >>> alignments obtained by different avenues in the Genome Browser do >> not >>> always agree. >>> >>> For example, go to: >>> >>> >>> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=170596672&o=66797792&t=66840262&g=refGene&i=NM_001037339 >> >>> and under mRNA alignment, this information appears: >>> >>> mRNA/Genomic Alignments >>> BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END >> >>> QUERY START END TOTAL >>> >> ----------------------------------------------------------------------------------------------------- >>> browser | 3876 100.0% 1 + 66797793 66840262 >>> NM_001037339 1 3876 3882 >>> >>> >>> But if you click on the link on this page: >>> >>> View details of parts of alignment within browser window. >>> >>> and look at the enumeration of the alignment with the genomic >> sequence >>> the mRNA begins at 66798504 (NOT 66797793)--although the sequence >>> appears to be the same. >>> >>> By other alignment approaches--i.e. BLAT of the relevant mRNA >> sequence, >>> one obtains the + 66797793 66840262 alignment. >>> >>> >>> Is this due to use of different versions of the human genome >> sequence? >>> Is there a cue that I am missing? >>> >>> Thanks, >>> >>> David Barker >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
