First of all, slurping a whole file into an array is usually a very bad idea. instead use

while(<FILE>){
#line is in $_
}
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Now, if you want to split on a tab, split on a tab. And..something is very wired over there, you split $_ but chomp $line (and don't assign $_ to $line...) You want something like:

while(<FILE>){
chomp;
my @columns=split /\t/;
$columns[0]=~tr/%//d; # When you want to get rid of single characters 
+tr/// should be better than s///
#do what ever you want with @columns..
}
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