Since you did not specify, I will assume your Regular file will contain the dashes. If this does not do what you want, then you must show the desired output: 
use strict;
use warnings;

open my $reg_out  , '>', 'RegularOligos.txt'   or die "can not open fi
+le RegularOligos.txt:$!";
open my $irreg_out, '>', 'IrregularOligos.txt' or die "can not open fi
+le IrregularOligos.txt:$!";
while(<DATA>){
    chomp;
    my @fields = split;
    my $line = join "\t", @fields;
    if ($fields[0] =~ /-/){
        print $reg_out "$line\n";
    }
    else{
        print $irreg_out "$line\n";
    }
}
close $irreg_out;
close $reg_out;

__DATA__
10002TU    AGACATTACCTGTGAGACACCTTTC   GCCTCCACCTCAGAGTCAG    TCCATGGG
+AAGGATCTCCGTGAAATCA
10002TU-2    GCTCCAGCTAGAAGAGAATCC    CCCACCAGGGCTGTGTAAG    CCTGTGAGA
+TAGTACAGCTGAAGAGTTGGC
10002TD    TGTGTTGATTCTCAGCCTCTTG    GACGGAGCACATAGGCAAAG    TCTGTTCTT
+CTCAGCTGTCTTTGTTGCTGC
10003TU    CAGCAAGCCCTGAGGTGTG    CAGTGAACTGAGAAAGACGAGAGG TGCAAGTCCAG
+ATGGAGGCCACC
10174TU-2    ACCTGAACAGCCTGACATGAAC   TGGGATGGAGGGCAAAGTC    CCACCTAGT
+ATGACCCAGCACACCTCC

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In reply to Re: separate data and print to two files by toolic
in thread separate data and print to two files by lomSpace

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