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 < michaelstei...@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 <g...@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 > > <michaelstei...@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 <g...@psu.edu> wrote: > >> > 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 > >> >> > > >> >> > >> >> ___________________________________________________________ > >> >> 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/ > >> > > >> > > >> > > >> > -- > >> > Graduate student, Bioinformatics and Genomics > >> > Makova lab/Galaxy team > >> > 505 Wartik lab > >> > University Park PA 16802 > >> > g...@psu.edu > >> > > > > > > > > > -- > > Graduate student, Bioinformatics and Genomics > > Makova lab/Galaxy team > > 505 Wartik lab > > University Park PA 16802 > > g...@psu.edu > > > -- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 g...@psu.edu
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