[BioC] Best way to get updated annotation for BACs

[Daniel Brewer]

Hello,

Sorry to come back onto this, but I can't get Lift Genome Annotations
(http://genome.ucsc.edu/cgi-bin/hgLiftOver) to work whatever I do.  Has
anyone else had any success with this tool? I always get "#Deleted in
new" for all the Clone's positions.  In fact, even if I try a test like
"Chr1:100000-100001", I get the same error.  Apologies for needing my
hand held on this one.

Dan

On 03/11/2010 5:11 PM, Sean Davis wrote:
> 
> 
> On Wed, Nov 3, 2010 at 9:49 AM, Daniel Brewer <daniel.brewer at icr.ac.uk
> <mailto:daniel.brewer at 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 at icr.ac.uk <mailto:daniel.brewer at icr.ac.uk>
>     > <mailto: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
> 
>     --
>     **************************************************************
> 
>     Daniel Brewer, Ph.D.
> 
>     Institute of Cancer Research
>     Molecular Carcinogenesis
>     MUCRC
>     15 Cotswold Road
>     Sutton, Surrey SM2 5NG
>     United Kingdom
> 
>     Tel: +44 (0) 20 8722 4109
> 
>     **************************************************************
> 
>     The Institute of Cancer Research: Royal Cancer Hospital, a
>     charitable Company Limited by Guarantee, Registered in England under
>     Company No. 534147 with its Registered Office at 123 Old Brompton
>     Road, London SW7 3RP.
> 
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> 

-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109

**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the a...{{dropped:2}}