Structure2.3.4 data file loading error

[Sri Kiran Reddy Alla]

Hello everyone,

I am new to Structure and trying to load my data file into STRUCTURE 2.3.4.

When I load this, 376 lines with 54581 columns, I am able to see the output. Data is loading without any error.

But, when I load this, 376 lines with 99187 columns, after clicking Proceed it is just blank page and data is not loading on Structure.

Please provide any inputs to resolve this issue. 

Thank you,

Kiran.

[Alberto Fameli]

I had a simar problem using 63,834 columns with SNP genotypes. I believe the problem is simply that STRUCTURE was not designed to handle so many markers. 

I recommend using fastStructure or the STRUCTURE-like analysis relying on the R package LEA. You can find a tutorial here:  

http://membres-timc.imag.fr/Olivier.Francois/tutoRstructure.pdf

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[Vikram Chhatre]

The number of markers STRUCTURE can handle is only limited by the memory of the machine it's running on. There is no upper limit coded into the program.

There are indeed many other tools which can do this analysis including ADMIXTURE (maximum likelihood) and many others that Alberto suggested. I recommend using the commandline version if for no other reason than to get a proper error message when things go wrong.

Good luck.

V

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