Hi Mike,

Would you mind sharing your history with me (g...@psu.edu) so that I can
take a look at what's going on? You can do this by selecting "Options ->
Share or Publish -> Share with a user" and entering my email address.

Thanks,
Guru.

On Thu, Mar 10, 2011 at 9:15 AM, Michael E. Steiper <
michaelstei...@gmail.com> wrote:

> Hi,
>
> 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
>
> Thanks,
>
> Mike
>
> 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.
> >
> > THANKS!
> >
> > Mike
> >
>
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-- 
Graduate student, Bioinformatics and Genomics
Makova lab/Galaxy team
505 Wartik lab
University Park PA 16802
g...@psu.edu
___________________________________________________________
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