Smartpca using Eigensoft
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10 weeks ago
rosy • 0

I am using eigensoft (smartPCA) to do PCA by

./smartpca.perl -i my.bed -a my.pedsnp -b my.pedind -o output.pca -p output.plot -e output.eval -m 10 -s 5 -l output.log

I also tried using example files in CONVERTF folder

./smartpca.perl -i example.bed -a example.pedsnp -b example.pedind -o output.pca -p output.plot -e output.eval -m 10 -s 5 -l output.log

but I got this error in both the cases

sh: smartpca: command not found

OOPS couldn't open file output.pca.evec for reading at ./smartpca.perl line 65. The eigensoft version I am using is latest(7.2.1) please help me to resolve this issue

smartpca • 187 views
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