while ( <DNAFILE> ) 
{            
    next if (/fixedStep chrom=chrX start=(.+) step=1/);
    $counter = $1;
}
print "$counter\t$_\n";
[download]

There are some issues with your code:

• if you find a heading-line, you leave the loop - the assignment $counter = $1 will not be executed in this case
• according to your spec you want to print all non-heading-lines => the print needs to be inside the loop
• you want to increase the counter with your lines => you need a statement line $counter++; somewhere

The following code might help you (untested!!)

while ( <DNAFILE> ) 
{
   if (/fixedStep chrom=chrX start=(.+) step=1/) 
        { 
          $counter = $1; 
        }
   else {
          print "$counter\t$_\n";
          $counter++;
        }
}
[download]

as you see, it is quite similar to your awk-code.

HTH, Rata