Probe ID to Sequence

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khadeeja ismail ▴ 400

@khadeeja-ismail-4711

Last seen 8.2 years ago

Hi, I need to find the following information for my IlluminaHumanMethylation450k probes but have no clue which packages I need. --Probe SNPs, SNP10 --UCSC refgene name, group and accession number. I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, GenomicFeatures as any related packages, but cannot see how I can use these. Any help is most appreciated. Best Regards, Hajja [[alternative HTML version deleted]]

SNPlocs GenomicRanges SNPlocs GenomicRanges • 1.7k views

ADD COMMENT • link updated 12.7 years ago by Tim Triche ★ 4.2k • written 12.7 years ago by khadeeja ismail ▴ 400

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Tim Triche ★ 4.2k

@tim-triche-3561

Last seen 3.6 years ago

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You could use BSgenome, Biostrings, and GenomicRanges for this, but since you did not ask about repeats, you could also use IlluminaHumanMethylation450kSNP, SNP10, and PROBELOCATION in the devel version (1.4.9) to get each :-) Thanks, --t On Aug 1, 2011, at 1:25 AM, khadeeja ismail <hajjja@yahoo.com> wrote: > Hi, > > I need to find the following information for my IlluminaHumanMethylation450k probes but have no clue which packages I need. > > --Probe SNPs, SNP10 > --UCSC refgene name, group and accession number. > > I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, GenomicFeatures as any related packages, but cannot see how I can use these. > > Any help is most appreciated. > > Best Regards, > Hajja [[alternative HTML version deleted]]

ADD COMMENT • link 12.7 years ago Tim Triche ★ 4.2k

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Chao-Jen Wong ▴ 580

@chao-jen-wong-3603

Last seen 9.3 years ago

USA/Seattle/Fred Hutchinson Cancer Rese…

Hi, Khadeeja, Accession number and regulatory group can be found in IlluminaHumanMethylation450k.db. Unfortunately this database package does not have snp10. The easiest way I found is exporting those information (snp10 and UCSC refname) along with the probe intensity data from GenomeStudio. If anyone has better solution, please let me know. As for for snp probes, you can easily tell from the probe IDs as snp probe ID always start with rsxxxx. Cheers, Chao-Jen ----- Original Message ----- From: "khadeeja ismail" <hajjja@yahoo.com> To: bioconductor at r-project.org Sent: Monday, August 1, 2011 1:25:54 AM Subject: Re: [BioC] Probe ID to Sequence Hi, I need to find the following information for my IlluminaHumanMethylation450k probes but have no clue which packages I need. --Probe SNPs, SNP10 --UCSC refgene name, group and accession number. I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, GenomicFeatures as any related packages, but cannot see how I can use these. Any help is most appreciated. Best Regards, Hajja [[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 -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org

ADD COMMENT • link 12.7 years ago Chao-Jen Wong ▴ 580

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It's in there, simply not exported (d'oh!!!). IF need be you can use IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10 IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND to do these things. (I recognize that I am somewhat of a bad person for suggesting it, but it's the least of my sins) Note the handy abbreviations for minimal typing. On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote: > Hi, Khadeeja, > > Accession number and regulatory group can be found in > IlluminaHumanMethylation450k.db. Unfortunately this database package does > not have snp10. The easiest way I found is exporting those information > (snp10 and UCSC refname) along with the probe intensity data from > GenomeStudio. If anyone has better solution, please let me know. > > As for for snp probes, you can easily tell from the probe IDs as snp probe > ID always start with rsxxxx. > > > Cheers, > Chao-Jen > > ----- Original Message ----- > From: "khadeeja ismail" <hajjja@yahoo.com> > To: bioconductor@r-project.org > Sent: Monday, August 1, 2011 1:25:54 AM > Subject: Re: [BioC] Probe ID to Sequence > > Hi, > > I need to find the following information for my > IlluminaHumanMethylation450k probes but have no clue which packages I need. > > --Probe SNPs, SNP10 > --UCSC refgene name, group and accession number. > > I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, > GenomicFeatures as any related packages, but cannot see how I can use these. > > Any help is most appreciated. > > Best Regards, > Hajja > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2@fhcrc.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]

ADD REPLY • link 12.7 years ago Tim Triche ★ 4.2k

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Good to know! Thanks!!! Wondering why they are not exported for they are important information for filtering purposes. Cheers, Chao-Jen ----- Original Message ----- From: "Tim Triche, Jr." <tim.triche@gmail.com> To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> Cc: "khadeeja ismail" <hajjja at="" yahoo.com="">, bioconductor at r-project.org Sent: Monday, August 1, 2011 2:25:12 PM Subject: Re: [BioC] Probe ID to Sequence It's in there, simply not exported (d'oh!!!). IF need be you can use IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10 IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND to do these things. (I recognize that I am somewhat of a bad person for suggesting it, but it's the least of my sins) Note the handy abbreviations for minimal typing. On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen < cwon2 at fhcrc.org > wrote: Hi, Khadeeja, Accession number and regulatory group can be found in IlluminaHumanMethylation450k.db. Unfortunately this database package does not have snp10. The easiest way I found is exporting those information (snp10 and UCSC refname) along with the probe intensity data from GenomeStudio. If anyone has better solution, please let me know. As for for snp probes, you can easily tell from the probe IDs as snp probe ID always start with rsxxxx. Cheers, Chao-Jen ----- Original Message ----- From: "khadeeja ismail" < hajjja@yahoo.com > To: bioconductor at r-project.org Sent: Monday, August 1, 2011 1:25:54 AM Subject: Re: [BioC] Probe ID to Sequence Hi, I need to find the following information for my IlluminaHumanMethylation450k probes but have no clue which packages I need. --Probe SNPs, SNP10 --UCSC refgene name, group and accession number. I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, GenomicFeatures as any related packages, but cannot see how I can use these. Any help is most appreciated. Best Regards, Hajja [[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 -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org _______________________________________________ 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 -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org

ADD REPLY • link 12.7 years ago Chao-Jen Wong ▴ 580

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The 1.4.9 version of the package hadn't passed the build check due to a bizarre bug in R CMD check, but now that I'm running it again with a more recent (r56301) build of R and updated Bioconductor packages, it appears to be checking out fine. I will re-upload it, but I would like to break the package into a lighter-weight annotations package and a heavier-weight probes package (with sequences instead of NuIDs) for the next real release. I'll ask Marc for another FTP password and see about getting (at least) 1.4.9 uploaded shortly. On Mon, Aug 1, 2011 at 4:20 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote: > Good to know! Thanks!!! Wondering why they are not exported for they are > important information for filtering purposes. > > Cheers, > Chao-Jen > > ----- Original Message ----- > From: "Tim Triche, Jr." <tim.triche@gmail.com> > To: "Chao-Jen Wong" <cwon2@fhcrc.org> > Cc: "khadeeja ismail" <hajjja@yahoo.com>, bioconductor@r-project.org > Sent: Monday, August 1, 2011 2:25:12 PM > Subject: Re: [BioC] Probe ID to Sequence > > It's in there, simply not exported (d'oh!!!). IF need be you can use > > > > IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP > > IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10 > > IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND > > > to do these things. (I recognize that I am somewhat of a bad person for > suggesting it, but it's the least of my sins) > > > Note the handy abbreviations for minimal typing. > > > > > > On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen < cwon2@fhcrc.org > wrote: > > > Hi, Khadeeja, > > Accession number and regulatory group can be found in > IlluminaHumanMethylation450k.db. Unfortunately this database package does > not have snp10. The easiest way I found is exporting those information > (snp10 and UCSC refname) along with the probe intensity data from > GenomeStudio. If anyone has better solution, please let me know. > > As for for snp probes, you can easily tell from the probe IDs as snp probe > ID always start with rsxxxx. > > > Cheers, > Chao-Jen > > > ----- Original Message ----- > From: "khadeeja ismail" < hajjja@yahoo.com > > To: bioconductor@r-project.org > > Sent: Monday, August 1, 2011 1:25:54 AM > Subject: Re: [BioC] Probe ID to Sequence > > > > > Hi, > > I need to find the following information for my > IlluminaHumanMethylation450k probes but have no clue which packages I need. > > --Probe SNPs, SNP10 > --UCSC refgene name, group and accession number. > > I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, > GenomicFeatures as any related packages, but cannot see how I can use these. > > Any help is most appreciated. > > Best Regards, > Hajja > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Chao-Jen Wong > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2@fhcrc.org > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > If people do not believe that mathematics is simple, it is only because > they do not realize how complicated life is. > > John von Neumann > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2@fhcrc.org > > > -- When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes. Derek Sivers <http: sivers.org="" berklee=""> [[alternative HTML version deleted]]

ADD REPLY • link 12.7 years ago Tim ▴ 160

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nb. The reason I mention this is that all problems of which I am aware are either marked as such (for problems which appear to be deeper than I am able to quickly address, such as RefGene:EntrezGene issues) or fixed (SNP, SNP10, STRAND, CPGS) in version 1.4.9 of the annotation package. On Mon, Aug 1, 2011 at 4:33 PM, Tim Triche, Jr. <ttriche@usc.edu> wrote: > The 1.4.9 version of the package hadn't passed the build check due to a > bizarre bug in R CMD check, but now that I'm running it again with a more > recent (r56301) build of R and updated Bioconductor packages, it appears to > be checking out fine. I will re-upload it, but I would like to break the > package into a lighter-weight annotations package and a heavier- weight > probes package (with sequences instead of NuIDs) for the next real release. > > I'll ask Marc for another FTP password and see about getting (at least) > 1.4.9 uploaded shortly. > > > On Mon, Aug 1, 2011 at 4:20 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote: > >> Good to know! Thanks!!! Wondering why they are not exported for they are >> important information for filtering purposes. >> >> Cheers, >> Chao-Jen >> >> ----- Original Message ----- >> From: "Tim Triche, Jr." <tim.triche@gmail.com> >> To: "Chao-Jen Wong" <cwon2@fhcrc.org> >> Cc: "khadeeja ismail" <hajjja@yahoo.com>, bioconductor@r-project.org >> Sent: Monday, August 1, 2011 2:25:12 PM >> Subject: Re: [BioC] Probe ID to Sequence >> >> It's in there, simply not exported (d'oh!!!). IF need be you can use >> >> >> >> IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP >> >> IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10 >> >> IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND >> >> >> to do these things. (I recognize that I am somewhat of a bad person for >> suggesting it, but it's the least of my sins) >> >> >> Note the handy abbreviations for minimal typing. >> >> >> >> >> >> On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen < cwon2@fhcrc.org > >> wrote: >> >> >> Hi, Khadeeja, >> >> Accession number and regulatory group can be found in >> IlluminaHumanMethylation450k.db. Unfortunately this database package does >> not have snp10. The easiest way I found is exporting those information >> (snp10 and UCSC refname) along with the probe intensity data from >> GenomeStudio. If anyone has better solution, please let me know. >> >> As for for snp probes, you can easily tell from the probe IDs as snp probe >> ID always start with rsxxxx. >> >> >> Cheers, >> Chao-Jen >> >> >> ----- Original Message ----- >> From: "khadeeja ismail" < hajjja@yahoo.com > >> To: bioconductor@r-project.org >> >> Sent: Monday, August 1, 2011 1:25:54 AM >> Subject: Re: [BioC] Probe ID to Sequence >> >> >> >> >> Hi, >> >> I need to find the following information for my >> IlluminaHumanMethylation450k probes but have no clue which packages I need. >> >> --Probe SNPs, SNP10 >> --UCSC refgene name, group and accession number. >> >> I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, >> GenomicFeatures as any related packages, but cannot see how I can use these. >> >> Any help is most appreciated. >> >> Best Regards, >> Hajja >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> Chao-Jen Wong >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., M1-B514 >> PO Box 19024 >> Seattle, WA 98109 >> 206.667.4485 >> cwon2@fhcrc.org >> >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> -- >> If people do not believe that mathematics is simple, it is only because >> they do not realize how complicated life is. >> >> John von Neumann >> >> -- >> Chao-Jen Wong >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., M1-B514 >> PO Box 19024 >> Seattle, WA 98109 >> 206.667.4485 >> cwon2@fhcrc.org >> >> >> > > > -- > When you emerge in a few years, you can ask someone what you missed, and > you'll find it can be summed up in a few minutes. > > Derek Sivers <http: sivers.org="" berklee=""> > > -- When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes. Derek Sivers <http: sivers.org="" berklee=""> [[alternative HTML version deleted]]

ADD REPLY • link 12.7 years ago Tim ▴ 160

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That is great, THANK YOU! Hajja --- On Mon, 8/1/11, Tim Triche, Jr. <ttriche@usc.edu> wrote: From: Tim Triche, Jr. <ttriche@usc.edu> Subject: Re: [BioC] Probe ID to Sequence To: "Wong, Chao-Jen" <cwon2@fhcrc.org> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>, "khadeeja ismail" <hajjja@yahoo.com> Date: Monday, August 1, 2011, 4:35 PM nb. �The reason I mention this is that all problems of which I am aware are either marked as such (for problems which appear to be deeper than I am able to quickly address, such as RefGene:EntrezGene issues) or fixed (SNP, SNP10, STRAND, CPGS) in version 1.4.9 of the annotation package. On Mon, Aug 1, 2011 at 4:33 PM, Tim Triche, Jr. <ttriche@usc.edu> wrote: The 1.4.9 version of the package hadn't passed the build check due to a bizarre bug in R CMD check, but now that I'm running it again with a more recent (r56301) build of R and updated Bioconductor packages, it appears to be checking out fine. �I will re-upload it, but I would like to break the package into a lighter-weight annotations package and a heavier-weight probes package (with sequences instead of NuIDs) for the next real release. I'll ask Marc for another FTP password and see about getting (at least) 1.4.9 uploaded shortly. On Mon, Aug 1, 2011 at 4:20 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote: Good to know! Thanks!!! Wondering why they are not exported for they are important information for filtering purposes. Cheers, Chao-Jen ----- Original Message ----- From: "Tim Triche, Jr." <tim.triche@gmail.com> To: "Chao-Jen Wong" <cwon2@fhcrc.org> Cc: "khadeeja ismail" <hajjja@yahoo.com>, bioconductor@r-project.org Sent: Monday, August 1, 2011 2:25:12 PM Subject: Re: [BioC] Probe ID to Sequence It's in there, simply not exported (d'oh!!!). IF need be you can use IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10 IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND to do these things. (I recognize that I am somewhat of a bad person for suggesting it, but it's the least of my sins) Note the handy abbreviations for minimal typing. On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen < cwon2@fhcrc.org > wrote: Hi, Khadeeja, Accession number and regulatory group can be found in IlluminaHumanMethylation450k.db. Unfortunately this database package does not have snp10. The easiest way I found is exporting those information (snp10 and UCSC refname) along with the probe intensity data from GenomeStudio. If anyone has better solution, please let me know. As for for snp probes, you can easily tell from the probe IDs as snp probe ID always start with rsxxxx. Cheers, Chao-Jen ----- Original Message ----- From: "khadeeja ismail" < hajjja@yahoo.com > To: bioconductor@r-project.org Sent: Monday, August 1, 2011 1:25:54 AM Subject: Re: [BioC] Probe ID to Sequence Hi, I need to find the following information for my IlluminaHumanMethylation450k probes but have no clue which packages I need. --Probe SNPs, SNP10 --UCSC refgene name, group and accession number. I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, GenomicFeatures as any related packages, but cannot see how I can use these. Any help is most appreciated. Best Regards, Hajja [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2@fhcrc.org _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2@fhcrc.org -- When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes. Derek Sivers -- When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes. Derek Sivers [[alternative HTML version deleted]]

ADD REPLY • link 12.7 years ago khadeeja ismail ▴ 400

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