Sorry, a correction (I had the lengths reversed):

Original .maf > maf to fasta > length is 5572544
Original .maf > CpG mask > maf to fasta > length is 2735329



On Thu, Mar 10, 2011 at 8:53 AM, Michael E. Steiper
<michaelstei...@gmail.com> wrote:
> Hi All,
> I have a general question about CpG masking.  I have a .maf file, when
> I use the maf to fasta tool, it gives me an alignment of 2,735,329 bp.
>  But if I CpG mask the .maf file (restricted definition) then I use
> the maf to fasta tool, I get a very different alignment length,
> 5,572,544 bp.  It would be great to know what is the cause of these
> differences.
> Mike

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