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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Apologies Michael, wrong answer to the wrong question! Please ignore and thanks for the heads up! jen On 3/18/11 10:22 AM, Jennifer Jackson wrote:

Hello Daniel,

Currently this is not possible through the Galaxy UI, but is is an excellent functionality suggestion that our team has been considering implementing.

As a work-around for now, all of the genomes in Galaxy come from external public sources: UCSC and others. The genome name/annotation tags should help you to find the source we used. If there is a particular genome that you are having trouble finding, please let us know and we can provide a direct pointer.

For future data questions, the mailing list galaxy-user@lists.bx.psu.edu would be a good choice. http://lists.bx.psu.edu/listinfo/galaxy-user

Thanks for using Galaxy!

Best,

Jen Galaxy team

On 3/10/11 5:53 AM, Michael E. Steiper 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org