Cpg Masking Changing Alignment Length?

Question: Cpg Masking Changing Alignment Length?

7.7 years ago by

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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modified 7.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.7 years ago by Michael E. Steiper • 20

7.7 years ago by

Michael E. Steiper • 20

Michael E. Steiper • 20 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

ADD COMMENT • link written 7.7 years ago by Michael E. Steiper • 20

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

ADD REPLY • link written 7.7 years ago by Guru Ananda • 60

7.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

Apologies Michael, wrong answer to the wrong question! Please ignore and thanks for the heads up! jen -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

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