[BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array

[Jinyan Huang]

Shirley,

I have done the alignment using BLAT as you mentioned. But there are
some tricks in it, for example, some probe sequence can map to
multiple genome positions. Some cannot map to any position. Using
different parameters will affect these results.

When you prepare the files, the BLAT is very fast. It will only take
less than 30mins.

On Thu, Jul 19, 2012 at 10:38 AM, shirley zhang <shirley0818 at gmail.com> wrote:
> Dear list,
>
> I am trying to retrieve the chromosome position/coordinates for each 25bp
> probe on Affymetrix Human Exon 1.0 array. I checked Affymetrix's website
> and found that Affymetrix only provides the genome position for each
> probeset/exon, and also provides the sequence information for each probe.
>
> I understand that I could first download the probe sequence from
> Affymetrix, and then BLAT them against Human Reference Genome to get the
> position. However, before I try BLAT, I am wondering whether anyone has
> already done the alignment using BLAT or other tools, and would like to
> share the probe position for each probe on Exon array. If the position is
> based on hg19/build 37, it would be more helpful.
>
> Thanks in advance!
>
> Shirley
>
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