$infile1 = "test1.bed"; $infile2 = "test2.bed"; $outfile = "merged.bed"; open ("IN1", "<$infile1") or die "Can't open $file: $!\n"; open ("IN2", "<$infile2") or die "Can't open $file: $!\n"; #open ("OUT", "<$outfile") or die "Can't open $file: $!\n"; my @array1; my $row = 0; my $col = 0; while () { chomp; my @info = split("\t"); @array1[$row]=@info; $row++; } print $array1[0][1];