[mira_talk] Re: MIRA vs Newbler (454 est's)
- From: Diogo Santos <diogofcul@xxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 25 Jul 2011 22:35:26 +0000
I think you hit the problem. My organism is a cross between two species of
plants and thus may be a great allelic diversity. But this explains the big
difference between MIRA and Newbler 2.5? Is it possible to rely on the results
of MIRA or in this case it is preferable to change parameters?
Sorry for the insistence ...
thanks
Diogo Santos
From: bach@xxxxxxxxxxxx
Subject: [mira_talk] Re: MIRA vs Newbler (454 est's)
Date: Mon, 25 Jul 2011 23:02:54 +0200
To: mira_talk@xxxxxxxxxxxxx
On Jul 25, 2011, at 17:19 , Diogo Santos wrote:I have received data from an
EST's project from 454. they make the assembly with Newbler 2.5 and they get
5869 contigs (length>100) with coverage 11x (I know it's low, but it's what I
get:( ). I try to use MIRA to make some testing and use the original data to
reassemble, but I get a strange result (19378 contigs with length >100 and
coverage 4x). Can you teel wich parameters should I change?
The number of contigs in an EST assembly can vary widely depending on several
factors.
First, make absolutely sure that he data you got in the SFF is preprocessed
correctly by the sequencing provider. I've seen just lately a data set where a
provider played around with the adaptors but did not tell the Roche
post-processing pipeline about it. The led to 1/3 of the reads still having
adaptor unclipped i the SFF ... and that is deadly.
Also, be really sure that MIDs are clipped away. Again, this is something the
provider normally should do as they *are* responsible to deliver correct data
as free as possible from sequencing artefacts.
Once you are sure your data is good, it's time to think about biological
explanations: is you organism multiploid with many differences between alleles?
If yes, then many people are taken by surprise that MIRA doesn't assemble that
together. MIRA is NOT a clusterer! It is an assembler and as such, it will
assemble the mRNA as it was in the cell.
Hope that helps, Bastien
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