SNP file input format

[Miriam H]

Hello,

I am trying to use STRUCTURE on SNP data (diploid), the data is
currently in genotype format for each SNP (i.e. AA, AG, GG). I am
unable to open a project a STRUCTURE because the data doesn't match
the subject and data parameters I specified. I looked into the sample
data file formats. It seems I need to convert genotypes to numerical
values? Do I need to include any other data?

[Vikram Chhatre]

Hi Mirium -

As you pointed out, the SNP genotypes will need to be converted to
numerical format. The create project dialogue will ask you a series
of questions about the parameters you wish to set. If you have
location and population information, you can add that to the main data
file and make appropriate references to it in the parameter set.

V

> --
> You received this message because you are subscribed to the Google Groups "structure-software" group.
> To post to this group, send email to structure...@googlegroups.com.
> To unsubscribe from this group, send email to structure-softw...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/structure-software?hl=en.
>

[Armghan Shahzad]

Dear Vikram Chhatre,

I have a similar type of question regarding data input format for SSR data which is in 1 and 0 format. The data is for wheat which is hexaploid. The individuals genotyped are from different geographical locations. Please guide me on
How can I prepare input data file which is acceptable in STRUCTURE?
What kind of analysis can I perform on this type of data?
Best Regards,

[Vikram Chhatre]

Hi Armghan,

The Structure user manual should answer most, if not all of your questions.  If then, you have any specific questions, someone here will be able to help you further.

Vikram

[Miriam Howard]

Hi Vikram,

Thanks for your response. I re-formatted my data (SNP, ploidy=2). I have 224 individuals (each with an id number) and 1536 x2 genotypes. So I have 3073 columns. The genotypes are single digit integers and my file is a tab delimited text file. 

However, when I try to create a project..I get an error that the data entries are not of the right number. The program expects 224 rows x 3073 entries. When I check my data by clicking on "Show Data File Format"  it states that my txt file has 224 lines and 3073 entries. 

The problem appears to be some incompatible formatting perhaps. Not sure what to try next. I am working on a MAC and downloaded STRUCTURE 2.3 For a mac. Any ideas or have you come across this before?

Thank you, Miriam

[Vikram Chhatre]

Mirium -

Did the program tell you how many rows and columns it found?  Also, does your file contain any extra information like population identifier, location identifier, recessive allele, etc?  Since those options occupy extra columns, you need to adjust your parameters accordingly.

Front-end versions of windows and mac should work very similar to each other.  The file formatting problems usually occur when you move files between platforms.  Utilities like dos2unix can help you with formatting the file with correct end of line character for the operating system in question.

V

[Nicole Veto]

Dear Miriam,

I also have this problem. Do you remember what was the resolution?

Or if anyone else has any suggestions, I appreciate it.

Thank you in advance for your reply.

Nicole.

> To unsubscribe from this group, send email to structure-software+unsub...@googlegroups.com.

> For more options, visit this group at http://groups.google.com/group/structure-software?hl=en.
>

--
You received this message because you are subscribed to the Google Groups "structure-software" group.
To post to this group, send email to structure...@googlegroups.com.

To unsubscribe from this group, send email to structure-software+unsub...@googlegroups.com.