input data files

[Prasanna Kankanala]

Hi Terry:

I have two excel files, one with the markers and associated genotypes for the cultivars and another one for disease severity for the cultivars. I am trying to get GWAS going to look for associations for disease resistance. This is my first time and I played with the tutorial data thus far. I am having error loading my files in tassel. Can you please let me know how I can make my files work in Tassel? The excel file with genotypes are numerical data (0-AA, 1-AB, 2-BB, NA - for no data) and phenotypes are numerical data scored on a scale from 1 to 10). 

Thanks, 

Prasanna

[Terry Casstevens]

Hi Prasanna,

Please review file formats at this document and let me know if you
have further questions.

http://www.maizegenetics.net/tassel/docs/Tassel_User_Guide_3.0.pdf

Best,

Terry

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[Prasanna Kankanala]

Hi Terry: 

I went through the manual. My question would be how do I convert my file into one of those acceptable files. I tried saving as a txt file and I still couldn't load them, I am attaching two files that I have for your reference. Thanks for your help. 

Prasanna

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[Nick Bell]

Hi Prasanna,

The first thing I would say is that as you are calling them 'excel' files there is a good chance that you need to make sure they are saved/exported as tab delimited text files (or .csv files its the same thing). 

In my expedience as a total beginner, Tassel should to be fine with any file extension, so long as the content meets it's expectations. I don't work with the 0/1/3 format, but I think you need to use a global search+replace to change those "N/A"'s to "N". 

I would also recommend you avoid excel altogether. Programs like notepad++ or text wrangler are much more useful, fast and stable when opening large datasets and performing search/replace etc. tasks.

You mention that you have played with the tutorial data, maybe you should do a side-by-side comparison between your data and the tute data, you may have some kind of miss-match in your header columns.

Good luck!

-Nick

[Terry Casstevens]

Hi Prasanna,

The discussion of converting data from one format to another can be
complicated, and I can't cover everything. Tassel's Hapmap format is
described in the User Guide. And using a combination of Excel,
editors, unix utilities, etc. your file can be converted to Hapmap.
Basically what needs to happen...

- Translate 0s to A (Homozygous A)
- Translate 2s to C (Homozygous C)
- Translate 1s to M (Het A / C)
- Translate NA to N (Unknown)

You also had some AAAB values which is probably errors but I
translated those to N

Then the whole matrix needs to be transposed because Hapmap has Taxa
as headers and sites as rows.

And there are fields in Hapmap that you don't have which can be added
with NA values.

In general, I will not have time to make these conversions but I did
convert this one file for you. No guarantees about correctness. You
should check for yourself.


Best,

Terry




On Thu, Mar 27, 2014 at 11:59 AM, Prasanna Kankanala

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