[mira_talk] Re: provide known repeats

On Wednesday 11 March 2009 Andreas Petzold wrote:
> the last assembly worked fine and now I have at least 3 % of my fish genome
> (simply too low coverage and to few data but I have to work with that). But
> I have another question (and maybe another feature): Is it possible to
> provide a file that contains already known repeats that should be
> considered for assembly ? Or if I masked the read with RepeatMasker first
> can mira use the information for assembly ?

Hi Andreas,

this is possible but requires some work to get the data ready to be fed in a 
certain way to MIRA. 

... then again ...

I first wanted to tell you how to create CAF files with all the data needed, 
but 
thinking of it I just came to the conclusion that it could be easier and 
faster if MIRA could read a file telling it to place tags at given positions 
into certain reads.

Should be not to difficult to implement, even if it's not on my TODO at the 
moment. Should I?

> On the other hand, is it neccessary ? Would it improve the repeat tackling

Perhaps. Perhaps not. This is rarely predictable. Unfortunately.

Regards,
  Bastien

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