[mira_talk] Re: force MIRA to produce only singletons and no debris

On Thursday 10 March 2011 21:44:11 Robin Kramer wrote:
> Singlet is an otherwise good read, that doesn't happen to have a match.
> Debris low quality clipped repeat and or Singlet.

Close enough to mine.

Well ... a "good" read is relative. I can show you reads which have perfect 
qualities but are (for whatever reason) completely junk. Having a distinction 
between "singlet" and "debris" therefore becomes sometimes muddy.

In think I started to shift and merge definitions some two years ago. Now, a 
singlet is any one-read-contig which end in the assembly, everything else is 
debris. That is: you can easily see singlets as contigified debris.

AFAIR, the newer versions of MIRA do not even report singlets anymore in the 
assembly info file ... I took them out because switches interfering with the 
creation of singlets made no singlet apear in an assembly and that tends to 
upset people (for whatever reason).

> I think the real issue, is that Mira info reported that there were no
> singlets in assembly info.

There you have it :-)

B.

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