If you really want to use ne, you have to check that the number of different elements equals the number of all the elements: 
for my $gene (@all_genes) {
    say $gene if @covered_genes == grep $_ ne $gene, @covered_genes;
}

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A benchmark shows your way, as inefficient as it might be, is about 15% faster.

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: grep not equal by choroba
in thread grep not equal by rnaeye

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