...
my $temp;        # declare $temp before the loop

while (...)
{
    ...
}

close FASTQIN;
my %count_seq;
open my $fh, ... # $temp is still in scope
...

##</code><code>##

$temp = $head . $seq;
print $temp;

##</code><code>##

close FASTQIN;
my %count_seq;

if (defined $temp)
{
    open my $fh, '<:encoding(UTF-8)', $temp or die "Cannot open $temp $!";

    while (<$fh>)
    {
        ...
    }
}