[mira_talk] Re: Hash frequency specification (precomputation)

  • From: Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 24 Oct 2011 11:28:13 -0400

Dear Evan,
   Thanks.

I'm trying to tell Mira what the HAF levels to use based on an analysis of a large set of sequencing data. I'm working on a eukaryotic genome where I've precomputed the frequency of occurrence for every 31mer spaced 3 bp apart. Mira can't assemble the whole thing at once, so I have to do it in pieces.

   Cheers,
   Bob

Evan wrote:
Bob, try looking at the asm/info/*.high_info_readrepeats.lst
file. You can read about the different HAF levels in the manual under the nrr/fer* parameters.


On Sun, Oct 23, 2011 at 3:56 PM, Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx <mailto:bruc@xxxxxxxxxxxxxxxxxxxxx>> wrote:

    Dear Bastien,
        I understand -- thanks anyway.

        Does the hash data get written to the log directory?


        Cheers,
        Bob

    Bastien Chevreux wrote:
    On Oct 23, 2011, at 22:44 , Robert Bruccoleri wrote:
    Is this clear?
    Crystal.

    The answer is still no, sorry. While in theory one could think of a 
mechanism to let MIRA use - under some circumstances - substitute files for the 
hash statistics (which you would need to generate as well, and it's not only 
k-mer frequencies in there but also positioning and a couple of other things), 
I fear that the changes to the code are non trivial to implement / integrate. 
And at the moment I have so many other burning areas that I won't have any time 
to spend on this kind of problem, sorry again.

    B.



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