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PED & MAP file extension

Hi everyone,

I'm trying to upload the PED & MAP file (tab-delimited file) into gplink to run the association test but it doesn't seem that it recognize it? I feel I'm missing some steps in between?! I followed the instruction on plink site on how to create PED & MAP file. How can I convert the txt format into Ped, MAP extension file so I can work on them?

Any thoughts are appreciated.

map plink plink ped
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updated by Ram Ram • written by Rakan • Rakan

it doesn't seem that it recognize it

What error do you receive? PED and MAP file are text files..

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updated by Ram Ram • written by alesssia alesssia

I'm receiving this error plink cannot execute this command locally

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updated by Ram Ram • written by Rakan • Rakan

And what is this command? Perhaps giving us some more context (how the file are formed, which command are you running, the precise error you receive...) will help us in replying :)

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written by alesssia alesssia

You can do one thing easily if you've a small data set, just format your data set into hapmap format and import in TASSEL and export for plink input.

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updated by Ram Ram • written by kumar.vinod81 kumar.vinod81

1 answer

Hi!

A good thing to do when using new software is to use the example data that is usually provided with it.

If you give a look at this page you will see there is a data set: http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml

If you have the same error message with the example data, then the problem is not (as I suspect) a problem of file format.

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updated by Ram Ram • written by Fabio Marroni Fabio Marroni

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