I'm not quite sure what you want to do with the files, but reading the file in a two-dimensional array can be done this way: 
use warnings;
use strict;
open my $filehandle, "<", "filename.bed" or die "open: $!\n";
my @data;
while (<$filehandle>) {
 chomp; # remove the line ending character
 push @data, [ split /\t/ ]; # split the rest and append it to our dat
+a
};

print $data[0]->[0];
# access the first element of the array
# it's a reference, "->" dereferences it
# at last, access the first element of the dereferenced array

[download]

Here the [] brackets create an anonymous array reference (not just an array) filled with the return value of split and this reference (which is a scalar value, so it can be stored in the array) is pushed to the array.

You can always use Data::Dumper to print the contents of your data structure. Read perlreftut and perldsc for more information on references and complex data structures.

Edit: forgot to chomp
Sorry if my advice was wrong.

In reply to Re: Creating 2D array / Matrix by aitap
in thread Creating 2D array / Matrix by kash650

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