PGDspider input file

[石勇]

Hi, everyone.

 I want to generate input files for structure by PGDspider. 

However, I fail to generate input files from fasta and nexus files.

Would you mind give me some better solutions?

Thanks in advance!

[Vikram Chhatre]

I am assuming your Fasta files contain sequences.  You will need to extract variant information from the sequences (genotypes) in order to use your data with Structure.

V

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[石勇]

HI,Vikram Chhatre 

 Thank you for your suggestion. 

 After extract the variant  sites as a fasta file from DnaSP, I cannot, however, to get the right input file.

All of the SNPs convert to "-9".

In SPID Editor, I selected the type of the data as SNP for "Parser Questions", and selected spcify data as "SNP" for "Writer Questions".

However, It still does't work.

Did I miss something?

I would be appreciated if you could help me to sort out the problem.

Thanks in advance.

The clips are my test data.

And the results shows like this:

'ALS1_A36_b' 1 -9

'ALS2_A36_a' 1 -9

'ALS2_A36_b' 1 -9

'ALS3_A36_a' 1 -9

'ALS3_A36_b' 1 -9

'ALS4_A36_a' 1 -9

'ALS4_A36_b' 1 -9

'ALS5_A36_a' 1 -9

'ALS5_A36_b' 1 -9

'ALS6_A36_a' 1 -9

'ALS6_A36_b' 1 -9

'ALS7_A36_a' 1 -9

'ALS7_A36_b' 1 -9

'ALS8_A36_a' 1 -9

'ALS8_A36_b' 1 -9

在 2014年5月8日星期四UTC+8下午9时48分41秒，Vikram Chhatre写道：

I am assuming your Fasta files contain sequences.  You will need to extract variant information from the sequences (genotypes) in order to use your data with Structure.

V

On Thu, May 8, 2014 at 9:41 AM, 石勇 <shi...@gmail.com> wrote:

Hi, everyone.

 I want to generate input files for structure by PGDspider. 

However, I fail to generate input files from fasta and nexus files.

Would you mind give me some better solutions?

Thanks in advance!

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在 2014年5月8日星期四UTC+8下午9时48分41秒，Vikram Chhatre写道：

I am assuming your Fasta files contain sequences.  You will need to extract variant information from the sequences (genotypes) in order to use your data with Structure.

V

On Thu, May 8, 2014 at 9:41 AM, 石勇 <shi...@gmail.com> wrote:

Hi, everyone.

 I want to generate input files for structure by PGDspider. 

However, I fail to generate input files from fasta and nexus files.

Would you mind give me some better solutions?

Thanks in advance!

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[Vikram Chhatre]

I am not familiar with the procedure for extracting variant information using DNASP.  How many variant sites do you have in your sequences?  Note that for diploid data, you will need information from both homologues in each individual.

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[zeamne T]

Hi Shiyong,

I've never tried to do it using DNAsp but i think you can use BWA and samtools to pull out the variants from your raw sequence data into a vcf file. PGD spider can then convert the vcf file into the structure input file.

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yujie