[BioC] Best way to get updated annotation for BACs

[Daniel Brewer]

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.

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 at icr.ac.uk
> <mailto:daniel.brewer at 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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Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
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Tel: +44 (0) 20 8722 4109

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