aitap's solution works fine, but I did a version using only 1 hash (and 1 array). 
#!/usr/bin/perl
use strict;
use warnings;

my (@genes, %tested);
while (<>) {
    s/^>//;
    
    my ($col1, $col2) = split;
    push @genes, $col1;
    $tested{$col2}++; 
}

{
    local $\ = "\n";
    for (@genes) {
        print if not $tested{$_};  
    }
}

[download]
When reading from the empty, <>, brackets, a file to read from has to be typed at the command line. For this program, I had the contents in file o33.txt. 
C:\Old_Data\perlp>type o33.txt
>chr9:133738100-133738472_0 chr20:62159728-62161126_840
>chr9:133738100-133738472_60    chr2:215589720-215676478_59220
>chr9:133738100-133738472_120   chr2:215589720-215676478_59160
>chr9:133738100-133738472_180   chr15:99500240-99507809_0
>chr9:133738100-133738472_240   chr2:215589720-215676478_59100
>chr9:133738100-133738472_253   chr1:162745876-162746210_215
>chr9:133747466-133747650_0 chr5:108523084-108532592_960
>chr9:133747466-133747650_60    chr20:62159728-62161126_900
>chr9:133747466-133747650_65

[download]
Then, my command line was the name of the program, t1.pl followed by the name of the file to read from, o33.txt.
perl t1.pl o33.txt

In reply to Re: NON Common Elements between two columns by Cristoforo
in thread NON Common Elements between two columns by Giorgio C

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