On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer <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

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