[mira_talk] Re: force MIRA to produce only singletons and no debris
- From: Artemus Harper <subanark@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 7 Apr 2011 09:42:36 -0700
Is there any verdict on using the iAssembler tool? I would assume you can
simply tweak mira's parameters to get more things to assemble together
rather than run mira 4 times in a row.
On Wed, Feb 16, 2011 at 1:59 PM, Sven Klages
<sir.svencelot@xxxxxxxxxxxxxx>wrote:
> 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
>
--
Artemus Harper
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