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.lstfile. 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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