[Arabidopsis] Re: seeking TAIR9 bpmap file for Arabidopsis tiling array 1.0R

alperyilmaz via arab-gen%40net.bio.net (by alperyilmaz from gmail.com)
Sat Oct 10 17:24:22 EST 2009


I just found TAIR8 bpmap in this location:
http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/download.htm

thanks,
alper

On Sep 17, 6:30 pm, Ann Loraine <alora... from gmail.com> wrote:
> Dear Colleagues,
>
> I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling array
> 1.0R probes onto the TAIR9 or TAIR8 genome sequence.
>
> (This is for setting up a demonstration server that will show labs how they
> can easily visualize and share tiling array and RNA-Seq data via the
> Integrated Genome Browser (igb.bioviz.org) and DAS, one of the deliverables
> for an NSF 2010 award, which started a year ago.)
>
> The array corresponds to GEO platform accession GPL1980. (If this is wrong,
> please let me know...the Web page for it is here:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980)
>
> The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet
> sure which genome it references. Probably it is the TAIR7 genome, but we
> haven't tested it as yet. The bpmap file that Affymetrix distributes
> references TAIR7 (what they call Jan 2004) and the company has no immediate
> plans to update it because their tiling array support relies on a genome
> being supported by the UCSC Genome Bioinformatics group, which only supports
> animal and some fungal genomes.
>
> If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R
> Array for TAIR9, or even TAIR8, I would be very grateful if you would give
> me their contact information or send me a link to the file.
>
> Also, if you are looking for such a file, please let me know, and I'll get
> in touch as soon as I find one...or as soon as we create it, if one cannot
> be found.
>
> Thank you very much for your time,
>
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and  Genomics
> UNC Charlotte




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