fastSTRUCTURE with haploid bacteria

[Amy Fleshman]

Hi,

I am looking to run fastSTRUCTURE on some haploid bacterial genomes. I'm wondering how I can make the input files from a SNP matrix full of As, Ts, Gs, and Cs. If I set up a new matrix with genome names in the first column and the SNP labels in the first row, could I then simply recode the nucleotide letters for numbers 1 (A), 2 (T), 3 (G), 4 (C) instead? Or would each genotype have to be different numbers/combinations?

Hopefully that made some sense. Anyway, any advice for running with haploid organism genomes would be greatly appreciated!!

Thanks so much,
Amy Fleshman
Center for Microbial Genetics and Genomics
Northern Arizona University

[Vikram Chhatre]

Hi Amy,

I am afraid you are stuck with having to use Structure for analyzing your data.

From the github page for FastStructure:

" Specifically, rows in the data file correspond to samples, with two rows per sample (note that only diploids are handled by this software), and columns correspond to SNPs. "

That said, take a look at PGDSpider software for converting between various data formats.  

V

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[Amy Fleshman]

Ah bummer. Thanks anyways. Especially for the quick response!

[Amy Fleshman]

Sorry meant to ask one last question: do you have a suggestion for which version of Structure I should use? There seems to be a couple, so I just want to make sure I'm starting off on the right foot. Thanks so much!

On Saturday, January 24, 2015 at 9:31:28 AM UTC-7, Vikram Chhatre wrote:

Hi Amy,

I am afraid you are stuck with having to use Structure for analyzing your data.

From the github page for FastStructure:

" Specifically, rows in the data file correspond to samples, with two rows per sample (note that only diploids are handled by this software), and columns correspond to SNPs. "

That said, take a look at PGDSpider software for converting between various data formats.  

V

On Fri, Jan 23, 2015 at 7:02 PM, Amy Fleshman <acf...@gmail.com> wrote:

Hi,

I am looking to run fastSTRUCTURE on some haploid bacterial genomes. I'm wondering how I can make the input files from a SNP matrix full of As, Ts, Gs, and Cs. If I set up a new matrix with genome names in the first column and the SNP labels in the first row, could I then simply recode the nucleotide letters for numbers 1 (A), 2 (T), 3 (G), 4 (C) instead? Or would each genotype have to be different numbers/combinations?

Hopefully that made some sense. Anyway, any advice for running with haploid organism genomes would be greatly appreciated!!

Thanks so much,
Amy Fleshman
Center for Microbial Genetics and Genomics
Northern Arizona University

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[Vikram Chhatre]

The latest one: 2.3.4

I recommend commandline version for large data sets.

V

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[Amy Fleshman]

Thanks so much!

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Amy Fleshman

Graduate Research Assistant

Center for Microbial Genetics and Genomics

Northern Arizona University

acf...@gmail.com

http://www.linkedin.com/pub/amy-fleshman/82/641/4a1/