[mira_talk] Re: denovo results clarifications
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 28 Mar 2010 17:30:46 +0200
On Freitag 26 März 2010 Stefano Ghignone wrote:
> Checking into the file *project*_int_clippings.0.txt, some of the
> already validated and re-sequenced 454 reads show these situation:
> [...]
> I also included the sanger sequences which should cover the same dna
>
> region, but they where excluded as well:
> > load: changed qual. 8-283f.ab1 Left: 15 Right: 865
> > load: unchanged mask. 8-283f.ab1 Left: 0 Right: 881
> > load: changed qual. 8-283r.ab1 Left: 15 Right: 930
> > load: unchanged mask. 8-283r.ab1 Left: 0 Right: 1008
> > load: changed minleft. 8-283f.ab1 Left: 15 -> 30
> > load: changed minleft. 8-283r.ab1 Left: 15 -> 30
> > proposed cutback 1a: left 8-283f.ab1 30 -> 33
> > skim detect: possible junk: 8-283f.ab1 [832,0
> > skim detect: possible junk: 8-283r.ab1 [900,0
> > proposed cutback: left 8-283f.ab1 865 -> 880
> > proposed cutback: left 8-283r.ab1 930 -> 1007
>
> ...it has been experimentally validated!!... :-(
This is ... interesting. For whatever reason, MIRA thinks it is a good idea to
cut back these reads. Why it thinks that I have no idea and needs to be
investigated.
Would the reads you have shown perhaps be very, very low coverage?
> How should I interpret these values and which are the settings I need to
> tune to let such reads be included into the assembly?
"-CL:pec=no"
However, I do not recommend this. It's one of the sharpest and most precise
weapons MIRA has against junk and it works wonders ... when it works, that is.
Would it be possible to get the data to see why MIRA fails on these?
Regards,
Bastien
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