Thank you for the help. Modified my code as: 

my %seen;

$/ = "";
while (<>) {
    chomp;
    my ($key, $value) = split ('\t', $_);

    my @lines = split /\n/, $key;
    my $key1 = $lines[1];

$seen{$key1}[Key] //= $key;
$seen{$key1}[Sum] += $value;



}
my $file_count = @ARGV;
foreach my $key1 ( keys %seen ) {
  
    if ( @{ $seen{$key1} } >= $file_count) {


        



        print join( "\t", @{$seen{$key1}});
        print "\n\n";
    }
}

[download]
but please help me also to have the name of the files in which a particular read exists. I mean with the total count it also tells me in which files it is present.

In reply to Re^2: merge multiple files giving out of memory error by Anonymous Monk
in thread merge multiple files giving out of memory error by Anonymous Monk

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