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Old 11-28-2014, 04:13 AM   #1
V.raeesi
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Location: Iran

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Question how i can use plink for chickens genotype-phenotype analysis???

I am performing a GWAS to detect genomic regions affecting imune responses in chickens! which corrections i must do for my analysis when i'm using plink for this study on chickens??? as you know chromosome numbers is different between human and chickens and by default plink performs commands base on 26 chromosomes ....
i need your helps.
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Old 11-29-2014, 07:18 AM   #2
chrchang
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As a general rule, PLINK help questions should be posted in the plink2-users Google group (https://groups.google.com/forum/#!forum/plink2-users ).

With that said, add --dog to use your data with PLINK 1.07 (chickens and dogs happen to have the same number of chromosomes). "--chr-set 38" also works in PLINK 1.9; see https://www.cog-genomics.org/plink2/input#chr_set .
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