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bim and fam downloaded as .txt files, won't work with PLINK?

Fair warning, I am very new to PLINK and to the command line in general. I downloaded my bed, bim, and fam files from this website. However, the bim and fam files are formatted as .txt files. As a result, when I type

plink --bfile dgrp2

it returns 'ERROR: No such file [ dgrp2.fam ] exists' because the file is named dgrp2.fam.txt. I tried renaming the files without the "txt" but it wouldn't let me. Advice would be greatly appreciated.

plink gwas snp
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updated by Biostar Biostar • written by maya123z • maya123z

1 answer

I recently discovered that macOS High Sierra did this on some downloaded files (and would also not allow me to rename affected files via finder). I think the best option is to open a terminal window, cd to the directory where these files are and then do mv dgrp2.fam.txt dgrp2.fam to rename the file. If that does not work then you may have to do sudo mv dgrp2.fam.txt dgrp2.fam

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written by GenoMax GenoMax

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

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written by WouterDeCoster WouterDeCoster

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