[mira_talk] Re: 87% redundancy in 454 paired-end reads
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 30 Nov 2010 23:35:58 +0100
On Dienstag 30 November 2010 Sònia Casillas wrote:
> Thanks so much, Bastien! This has given me a break! I couldn't
> understand why MIRA was taking so long time and huge RAM to assembly
> only one more run, and this is why!
Probably, yes. What I was thinking about: did you try to assemble just this
run? Perhaps even once with and once without paired-end info? My reasoning
would be: if that run was really that much redundant, then assembling just
those reads with a very high stringency would probably yield a very fragmented
assembly.
To that assembly you could then re-map the very same reads you used to build
it (a bit less stringent then) and then take from each cluster a couple of
reads (hand-picked) and their mate pairs (which may be in another contig) and
that could be an easy way to reduce your redundancy.
B.
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