[mira_talk] Re: force MIRA to produce only singletons and no debris
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Feb 2011 23:09:51 +0100
On Wednesday 16 February 2011 22:59:44 Sven Klages wrote:
> Just to give my 2p, .. though it is slightly off-topic.
Not at all, completely on-topic I'd say.
> 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.
They have a point there, but ... well, not always I think. In the end it's a
matter of how much "love" you want to put into curation of your data sets.
And I musst confess my "love" took a big dip when I was first confronted to
100m Solexa RNASeq reads ... I still haven't recovered yet.
B.
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