Thank you for taking the time to have a look; I have only been learning for 2 weeks. My %strands is as follows: 

$key = some ID
$value = + or -

[download]
If I print out $strands{$ID[$i]}, all it does is print a string of pluses and minuses.

I have however figured out the problem: 
my @ID;
foreach my $line(@col_NM) {
    if ($line =~ m/(NM\_\d+)/) {
    push (@ID, $1);         
    }    
}

[download]
If $line did not match /(NM\_\d+)/, it would not be added to @ID . Since, I iterate through $ID[$i], I became out of sync with my positives and minuses.

Thank you for pointing me in the right direction and your patience! :) El

In reply to Re^4: error calling variables? Going insane... by lecb
in thread error calling variables? Going insane... by lecb

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