Hi Michael, Apologies for the delay in response. The 'Mask CpG' tool currently supports pairwise alignments only, and it skips all blocks containing a single species. This is the reason why your masked output has fewer blocks compared to the input MAF file. We don't have immediate plans to extend the tool to >2-way alignments. If we are to do this, we'll let you know. Thanks for using Galaxy, and please let us know if you have any other questions. Guru. On Mon, Mar 14, 2011 at 10:02 AM, Michael E. Steiper < michaelsteiper@gmail.com> wrote:

Hi Guru

I had a look at the maf files (I am new to them, so this is just my guess). It looks like the maf to fasta in Galaxy removes all of the blocks that have only one species present. Does this look like the situation? Again, I am new to this file type.

Thanks for looking into this for me.

Best

Mike

On Mon, Mar 14, 2011 at 9:56 AM, Guru Ananda <guru@psu.edu> wrote:

...

Hi Mike, It looks like 'Mask CpG' tool is returning 13064 blocks out of the 17209 blocks in your input MAF file. This is perhaps why the sequence lengths before and after masking differ. We are trying to identifying the source of this issue. We'll keep you posted about the same. Sorry for any inconvenience this may have caused. Guru. On Thu, Mar 10, 2011 at 10:42 AM, Michael E. Steiper <michaelsteiper@gmail.com> wrote:

...

Dear Guru, Yes, of course. I just shared it with you. Best Mike

On Thu, Mar 10, 2011 at 10:30 AM, Guru Ananda <guru@psu.edu> wrote:

...

Hi Mike, Would you mind sharing your history with me (guru@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 <michaelsteiper@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 <michaelsteiper@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 guru@psu.edu

-- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 guru@psu.edu

-- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 guru@psu.edu