I know analysis using ssr data. but i want to analyze for SNP data. can anyone help in making input file for SNP data.
What is burnin periiod and how to fix this.
Hello dear Suvarna,
when you do SNP data run, it is same as SSR, however coding must be binary and missing always -9 or you can convert your raw data using PGDSpider software ver. 2.1.1.3
Use 10K burnin and 10K MCMC 5 iteration and K1 to K10
Hope this helps
Good Luck!
Regards,
Sveta
The SNP data’s (ATGC) can be converted into binary format (1234) and use structure program. To prepare run need to be considered SNP are bi-allele and burning period based on your total SNPs ( if you want to reduce time).
How to convert SNP datas rows to columns and columns to rows. as it contains ATGC and i tried in SPSS to convert but couldnot get. i want input file for structure analysis.
how to convert it into binary format
In SNP data, Columns contains Genotypic sequence and rows contains sequence of loci. so i want reverse to feed as input for structure software. so how to do this.
If your data is small, you can do it manually by excel using paste special option.
It is huge and more no of rows 80920 .it is not possible in excel. I want to run structure software. Can I have satishkumar natarajan email I'd so that I can explain
Better to use Admixture software for SNP or might be fastSTRUCTURE
First you have to convert the SNP raw file into binary format by using PGDSspider software then start the STRUCTURE
Mahesh Damodhar Mahendrakar I used PGDSspider to convert .vcf to structure, but I need this file in .geno or another for run structure... do you know how make that?
Hi i came across your discussions from two years ago and now I'm also working on large SNP data set using Structure software. May I know how you solve the problems of transposing the data into binary format?
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