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my @one = split /,/, '1,2,3,4,5,6';
my @two = split /,/, '2,9,8,4,7,6';
...

__END__
-1,-7,-5,0,-2,0

use List::MoreUtils qw(pairwise);

...

our ($a, $b);  # keep warnings happy
my $result = join ',', pairwise { $a - $b } @one, @two;