[mira_talk] Re: 454 homopolymers
- From: Leonor Palmeira <mlpalmeira@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Mar 2011 13:26:56 +0100
On 23/03/11 10:11, Leonor Palmeira wrote:
On 22/03/11 20:29, Sandrine Moreira wrote:
Hi,
Has anyone try to use some denoiser tools such as Ampliconnoise ?
No, I haven't tried using PyroNoise (the actual tool for noise reduction
in Ampliconnoise). I'll have a look at that.
The way I understand PyroNoise works is that it creates an alignment of
similar flowgrams and then infers a consensus sequence based on the
flowgrams of the alignment. This gives a reduced denoised dataset where
similar reads are merged into one "denoised-read".
Using the data as output by PyroNoise will therefore not do the job, as
the coverage estimation will be severely underestimated for regions
where a denoised-read summarizes a large number of original reads. This
is not good for MIRA, where the coverage estimation is a key step.
We could of course re-build a dataset where each denoised-read will be
present as many times as the reads it is inferred from. But then comes
my second concern: PyroNoise does not seem to output a quality file for
the "denoised-reads". This seems much more problematic...
Has anyone had any experience with PyroNoise, namely on these two issues?
Leonor.
--
Leonor Palmeira, PhD
Phone: +32 4 366 42 69
Email: mlpalmeira AT ulg DOT ac DOT be
http://sites.google.com/site/leonorpalmeira
Immunology-Vaccinology, Bat. B43b
Faculty of Veterinary Medicine
Boulevard de Colonster, 20
University of Liege, B-4000 Liege (Sart-Tilman)
Belgium
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