obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
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shirley zhang ★ 1.0k
@shirley-zhang-2038
Last seen 10.2 years ago
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]]
Alignment probe Alignment probe • 2.7k views
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@james-w-macdonald-5106
Last seen 4 hours ago
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Hi Shirley, Does this have what you want? http://bioconductor.org/packages/2.10/data/annotation/html/HuExExonPro besetLocationHg19.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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: 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
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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? Thanks again, Shirley On Thu, Jul 19, 2012 at 9:11 AM, James W. MacDonald <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]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**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 > > [[alternative HTML version deleted]]
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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 particularly section 8, 'Finding all the patterns of a constant width dictionary in an entire genome'. Best, Jim > > Thanks again, > Shirley > > On Thu, Jul 19, 2012 at 9:11 AM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Shirley, > > Does this have what you want? > > http://bioconductor.org/packages/2.10/data/annotation/html/HuExE xonProbesetLocationHg19.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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > 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 > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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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/d oc/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 at="" uw.edu="">> <mailto:jmacdon at="" uw.edu="">> wrote: >> >> Hi Shirley, >> >> Does this have what you want? >> >> >> http://bioconductor.org/packages/2.10/data/annotation/html/HuExExon ProbesetLocationHg19.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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> 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 at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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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="" pac="" kages="" 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="" packag="" es="" 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]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >>> > >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https :="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.**science.biology.informatics.** >>> 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 > -- Xiaoling (Shirley) Zhang M.D., Ph.D. Boston University, Boston, MA Tel: (857) 233-9862 Email: zhangxl@bu.edu [[alternative HTML version deleted]]
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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="" pa="" ckages="" 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="" packa="" ges="" 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]] >>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >>>> > >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<http s:="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.**science.biology.informatics.** >>>> 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 >> > > [[alternative HTML version deleted]]
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Jinyan Huang ▴ 190
@jinyan-huang-4157
Last seen 10.2 years ago
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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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