On Wed, Nov 3, 2010 at 9:49 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote:

> That's great, many thanks for that.  The only problem I am having is
> that some of the clones do not come up in the bacEndPairs table, for
> example RP11-363L4 or CTD-2001A18.  When I search for these in Ensembl
> they sometimes are there as a sequence, but sometimes not. Any ideas?
> The non-matching clones are about two thirds of the set.
>
>
That figures....

Do you have the original design file with genomic locations?  If so, use the
UCSC liftover tool to go from the old genome to the genome of your choice.
 Have the arrays been used in a published experiment?  If so, the design
file may be available via NCBI GEO or ArrayExpress.

Sean



> Many thanks
>
> Dan
>
> On 03/11/2010 12:02 PM, Sean Davis wrote:
> >
> >
> > On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer <daniel.brewer@icr.ac.uk
> > <mailto:daniel.brewer@icr.ac.uk>> wrote:
> >
> >     Hello,
> >
> >     I am dealing with a BACs microarray, but the annotation I have is
> from
> >     an old version of the human genome.  Could anyone suggest some ways
> of
> >     updating the information to hg19?  I would initially like the
> positional
> >     information, but also want gene(s) the BAC covers and whether the BAC
> >     covers the whole gene or whether it is at the front or back.  For
> each
> >     BAC I have a clone name e.g. RP11-172L12 and a ChoriID N0172L12.
> >
> >
> > Hi, Daniel.
> >
> > Check out the bacEndPairs track at UCSC.  The name column will contain
> > the clone name.  You could use the table browser to get the data that
> > you want or just download the whole table.  A workflow of rtracklayer
> > track downloads into IRanges objects of one type or another for genes
> > and bac-ends would allow you to get the overlap of bac-ends with genes;
> > I don't have details at hand, but the data sources are easily available.
> >
> > Sean
>
> --
> **************************************************************
>
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
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