[Genome] trouble mapping BAC clone

[Andrew Yee]

Thanks for looking into this!

On Nov 28, 2007 3:46 PM, Archana Thakkapallayil <archanat at soe.ucsc.edu>
wrote:

> Hello Andrew,
>
> I have forwarded your question to one of our developers and here is the
> response:
>
> This appears to be a problem of changing formats in NCBI files we use
> during the construction of these tracks and a confusion in the data in
> the file that we used to relate the clone id to the STS marker id.
>
> For the Hg17 STS markers and fish clone data, the file we obtained in
> July 2004 had the line:
> 8 RP11-128G18 C 8q24.1(FHCRC) SHGC-20519 29800 NT_008046
>
> For the Hg18 STS markers and fish clone data, the file we obtained in
> January 2006 had the line:
> 8 RP11-128G18 C 8q24.1(FHCRC) chr8 127Mb D8S1813 UniSTS:29800
>
> This file is currently obtained from the WEB site:
> http://www.ncbi.nlm.nih.gov/genome/cyto/cytobac.cgi?CHR=all&VERBOSE=ctg
>
> And when I extract the data from that WEB site today, this line reads:
> 8 RP11-128G18 C 8q24.1(FHCRC) chr8 127Mb SHGC-20519 UniSTS:29800
>
> This file is used to relate the clone id RP11-128G18 to the STS marker
> id of SHGC-20519. But in the data we obtained in January 2006 had this
> clone id related to the STS marker id of D8S1813 which is indeed another
> alias name for SHGC-20519, but this wasn't recognized during our
> processing as the same BAC end so we missed it due to naming confusion.
>
> To fix this would require some work in our procedures to account for the
> potential different names given to us in NCBI files. We might consider
> fixing it for the next go-around of STS markers, FISH clones, and BAC
> ends.
>
> As a work around, you could BLAT the sequence for this clone that is
> present on hg17 at position chr8:127,751,255-127,751,581 against the
> hg18 assembly. You'll get a 100% match at the same location on hg18.
>
> I hope this information is helpful to you. Please don't hesitate to
> contact us again if you require further assistance.
>
> Regards,
>
> Archana
> UCSC Genome Bioinformatics Group
>
> Andrew Yee wrote:
> > Hi, sorry for the utter naiveness of the question, but I've been having
> > trouble mapping the BAC clone RP11-128G18.
> >
> > I can find it here:
> >
> > *
> >
> http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=8&MAPS=ugHs,genes,clone-r&cmd=focus&fill=40&query=uid(26982648)&QSTR=RP11%2D128G18
> > *<
> http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=8&MAPS=ugHs,genes,clone-r&cmd=focus&fill=40&query=uid(26982648)&QSTR=RP11%2D128G18
> >
> >
> > but can't seem to find it when using the Table Browser.
> > Thanks,
> > Andrew
> > _______________________________________________
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> >
>