Genes to SNPs Tool

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Voke AO ▴ 760

@voke-ao-4830

Last seen 9.6 years ago

Hi all, Is there a tool in R that can give me a list of associated SNPs when I my input is a list of genes. I had a look at biomaRt manual...but I wasn't quite sure of a way forward. Any suggestions will be greatly appreciated. Thanks. Avoks

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ADD COMMENT • link updated 11.9 years ago by Yong Li ▴ 80 • written 11.9 years ago by Voke AO ▴ 760

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Wang, Li ▴ 180

@wang-li-5216

Last seen 9.6 years ago

Hi, all I have transcriptomes of 31 samples. I have detected SNPs for each sample compared to Reference genome. My goal is to detect common SNPs among all the 31 samples based on 31 tables of SNPs (each sample vs reference genome). I am writing to ask if there is a bioconductor package which can achieve my goal. Thanks! Li

ADD COMMENT • link 11.9 years ago Wang, Li ▴ 180

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Think you are better off using something "like" GATK -which has a Bayesian algorithm where you get more power to detect SNPs by adding more samples. FYI Since you have transcriptones you might have to watch standed-ness issues depending on the expt protocol you have. ... That said samtools mpileup will probably work just as well and even vcftools with a simple vcf merge may even be all you need? Those hi-throughput "workhorse" packages will probably be better for such a task. We use bioconductor extensively for NGS analysis but not the SNP/indel calling specifically. Rsamtools has an R interface to many of these operations and you will also need to understand the GenomicFeatures package to get full benefit. Cheers Paul -----Original Message----- From: Wang, Li <li.wang@ttu.edu> To: bioconductor at r-project.org <bioconductor at="" r-project.org=""> Subject: [BioC] SNP detection of multiple samples Date: Wed, 23 May 2012 16:29:54 -0500 Hi, all I have transcriptomes of 31 samples. I have detected SNPs for each sample compared to Reference genome. My goal is to detect common SNPs among all the 31 samples based on 31 tables of SNPs (each sample vs reference genome). I am writing to ask if there is a bioconductor package which can achieve my goal. Thanks! Li _______________________________________________ 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

ADD REPLY • link 11.9 years ago Paul Leo ▴ 970

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Hi, Paul Thanks for your reply. I will look into those packages and select the suitable one for exploration. Cheers Li ________________________________________ From: Paul Leo [p.leo@uq.edu.au] Sent: Wednesday, May 23, 2012 11:45 PM To: Wang, Li Cc: bioconductor at r-project.org Subject: Re: [BioC] SNP detection of multiple samples Think you are better off using something "like" GATK -which has a Bayesian algorithm where you get more power to detect SNPs by adding more samples. FYI Since you have transcriptones you might have to watch standed-ness issues depending on the expt protocol you have. ... That said samtools mpileup will probably work just as well and even vcftools with a simple vcf merge may even be all you need? Those hi-throughput "workhorse" packages will probably be better for such a task. We use bioconductor extensively for NGS analysis but not the SNP/indel calling specifically. Rsamtools has an R interface to many of these operations and you will also need to understand the GenomicFeatures package to get full benefit. Cheers Paul -----Original Message----- From: Wang, Li <li.wang@ttu.edu> To: bioconductor at r-project.org <bioconductor at="" r-project.org=""> Subject: [BioC] SNP detection of multiple samples Date: Wed, 23 May 2012 16:29:54 -0500 Hi, all I have transcriptomes of 31 samples. I have detected SNPs for each sample compared to Reference genome. My goal is to detect common SNPs among all the 31 samples based on 31 tables of SNPs (each sample vs reference genome). I am writing to ask if there is a bioconductor package which can achieve my goal. Thanks! Li _______________________________________________ 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

ADD REPLY • link 11.9 years ago Wang, Li ▴ 180

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Yong Li ▴ 80

@yong-li-5277

Last seen 9.6 years ago

Hi Ovokeraye, not sure how would you define "associated SNPs". If you meant the SNPs located in the gene, then the code in my previous post using BiomaRt can do the job. https://stat.ethz.ch/pipermail/bioconductor/2012-May/045521.html My problem was that with 50 genes it will not work. But with 10 or 20 genes it works. Hope that helps. Yong On Wed, May 23, 2012 at 10:25 PM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Hi all, > > Is there a tool in R that can give me a list of associated SNPs when I my input is a list of genes. I had a look at biomaRt manual...but I wasn't quite sure of a way forward. > > Any suggestions will be greatly appreciated. > > Thanks. > > Avoks > > _______________________________________________ > 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

ADD COMMENT • link 11.9 years ago Yong Li ▴ 80

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