On Mon, Nov 17, 2008 at 1:53 PM, Al Tango <time.is.flying@gmail.com> wrote:

> Not sure if this needs using Bioconductor.
>
> To get the chromosome position(in bp, Build36) for a BAC clone, eg
> 'RP11-189K9', I was following this post:
>
> http://article.gmane.org/gmane.science.biology.informatics.conductor/11360/match=bac+position
>
> But I only got this table:
> '
> ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/BUILD.36.1/initial_release/clone.q.gz
> '
>
> (Here is the first several lines of the table:
> #tax_idclone_id  xref_idclone_name insert_accession     insert_gi strain
>
> 9606    CloneID:1               RP11-1006M13
> 9606    CloneID:10              CTA-102N2
> 9606    CloneID:100     CTA-124G2
> )
>
> from which I can identify the CloneID '230700' for 'RP11-189K9',
> without any positional information;
> Where to go to get the additional dataset for positions, please?
>


Why not use the BacEndPairs table at UCSC?

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/bacEndPairs.txt.gz

Lists BAC name and location.

Sean

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