[mira_talk] Re: force MIRA to produce only singletons and no debris
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Feb 2011 22:59:44 +0100
2011/2/16 Jeremy Volkening <volkening@xxxxxxxxxxxxx>
> On Wed, 2011-02-16 at 21:19 +0100, Bastien Chevreux wrote:
>
> > Now on to why I think this kind of iterational assembly is a bad idea:
> > you lose accuracy ... a lot. Consider a case where you perhaps have a
> > ploidy variants with one column having 50 T's and 50 A's and one C
> > (the A and T being real, let's a ssume the C is a sequencing error).
>
Just to give my 2p, .. though it is slightly off-topic. People are asking me
the same questions as the OP, they want less contigs and care about the
debris / singleton stuff with medium sized 454 EST datasets (300,000 -
1,000,000 reads). Depending of the library and the dataset, there are some
50%-90% of the reads assembled into contigs. They do care about the rest ...
thus asking if there is a way to get these reads assembled too (some check
with blast if the reads hit contigs). If then the reads are blasted against
nrprot or something similar, it is not really important if there is an "A"
or an "T" at that position for characterising the potential transcript ...
that is the "usual" argumentation.
So people tend to re-assemble the assemblies ... this is one "re-Assembler"
using MIRA and cap3 (I have not tested this package),
http://bioinfo.bti.cornell.edu/tool/iAssembler/
cheers,
Sven
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