Dear Herve, James and Jinyan,

Finally I got what I want from UCSC ftp server. They do provide probe-level
coordinates (hg19)

Thanks though for all your suggestions.

Shirley

On Thu, Jul 19, 2012 at 10:18 PM, shirley zhang <shirley0818@gmail.com>wrote:

> Hi Herve, James and Jinyan,
>
> Thank you all for your suggestions. I will try them.
>
> Shirley
>
> On Thu, Jul 19, 2012 at 3:56 PM, Hervé Pagès <hpages@fhcrc.org> wrote:
>
>> Hi Shirley, James,
>>
>>
>> On 07/19/2012 07:15 AM, James W. MacDonald wrote:
>>
>>> Hi Shirley,
>>>
>>> On 7/19/2012 10:02 AM, shirley zhang wrote:
>>>
>>>> Thanks Jim for your information.
>>>>
>>>> The package you pointed out only provides the Exon-level probeset
>>>> chromosome location. What I want is probe-level chromosome location.
>>>> For each 25bp probe, Affymetrix provides its sequence, and positionX
>>>> and positionY on the Chip, but not the position on Human reference
>>>> genome.
>>>>
>>>> Do you have any other suggestions? Does package GenomeFeatures have
>>>> this functionality?
>>>>
>>>
>>> No, that package is designed to deal with already aligned data (for
>>> which you would already have the data you desire).
>>>
>>> I would recommend using Biostrings and the requisite BSgenome package.
>>> Aligning fixed width sequences with no indels or mismatches is much
>>> simpler than the typical alignment problem, for which matchPDict() is
>>> ideally suited.
>>>
>>> Please see
>>>
>>> http://bioconductor.org/**packages/2.10/bioc/vignettes/**
>>> BSgenome/inst/doc/**GenomeSearching.pdf<http://bioconductor.org/packages/2.10/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf>
>>>
>>>
>>> particularly section 8, 'Finding all the patterns of a constant width
>>> dictionary in an entire genome'.
>>>
>>
>> I think the matchAffyProbes() function in the altcdfenvs package (which
>> is based on matchPDict()) does that too and might be a little bit more
>> convenient to use.
>>
>> Cheers,
>>
>> H.
>>
>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>
>>>> Thanks again,
>>>> Shirley
>>>>
>>>> On Thu, Jul 19, 2012 at 9:11 AM, James W. MacDonald <jmacdon@uw.edu
>>>> <mailto:jmacdon@uw.edu>> wrote:
>>>>
>>>>     Hi Shirley,
>>>>
>>>>     Does this have what you want?
>>>>
>>>>
>>>> http://bioconductor.org/**packages/2.10/data/annotation/**html/**
>>>> HuExExonProbesetLocationHg19.**html<http://bioconductor.org/packages/2.10/data/annotation/html/HuExExonProbesetLocationHg19.html>
>>>>
>>>>
>>>>     Best,
>>>>
>>>>     Jim
>>>>
>>>>
>>>>
>>>>
>>>>     On 7/18/2012 10:38 PM, shirley zhang 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
>>>>
>>>>                 [[alternative HTML version deleted]]
>>>>
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>>>> >
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>>>> conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>>
>>>>
>>>>     --     James W. MacDonald, M.S.
>>>>     Biostatistician
>>>>     University of Washington
>>>>     Environmental and Occupational Health Sciences
>>>>     4225 Roosevelt Way NE, # 100
>>>>     Seattle WA 98105-6099
>>>>
>>>>
>>>>
>>>>
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages@fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>
>

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