plink scoring output for multiple files
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2.4 years ago
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Hi all, I am using plink to create a profile score for multiple genes present in aorta tissue. I wrote the names of the input files for the plink command in the separate file and wrote a simple script which loops in the input files and run the plink command on it. The code is as follows: for FileName in $(cat testFileNames.txt); do plink --bfile 1000G_20101123_v3_281K_bestguess_thres0_chr1_X_280311_1586_1142_797_Populationcontrols --score $FileName 1 2 4; done

But the above code is generating the scoring profile named "plink.profile" only for the last file, whose name is present in the testFileNames.txt. For example, the testFileNames.txt contains

Artery_Aorta.ENSG00000000460.12.wgt.RDat.txt
Artery_Aorta.ENSG00000000971.11.wgt.RDat.txt

The above command would generate only a single .profile file listing the values for the Artery_Aorta.ENSG00000000971.11.wgt.RDat.txt gene. I would have expected the command to generate a separate .profile output files for each of the input file. Is there some way around for it as I need to generate the scores for 6000 genes?

Best.

SNP genome plink allele scoring • 639 views
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