[mira_talk] Re: 454 homopolymers
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Mar 2011 22:19:10 +0100
On Wednesday 23 March 2011 14:05:06 Leonor Palmeira wrote:
> I'm using MIRA V3.2.0 (production version).
Good enough.
> Note to self: do not use 454 alone on future assembly projects! :-)
Very important note. Put it on a sticker (or better: 100 stickers) and spread
the word :-)
> I'm not sure the consensus calling in MIRA can be improved without using
> the flowgrams. The problem with the .fasta extracted from the .sff
> files, is that they contain reads in a discrete space (A present or not)
> whereas the flowgrams are in a continous space (A is present with
> intensity 0.45).
Yvan noted that in his opinion, Newbler still had less indels when working
just on FASTA+QUAL than MIRA. That is something I'd like to stop ;-)
> I will prepare some data for you with some "nice" regions where I have
> identified homopolymer problems, so you can have a look.
Thanks.
B.
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