[mira_talk] Re: Multiple long repeats in genome.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 20 Mar 2011 14:11:19 +0100
On Thursday 17 March 2011 18:40:27 Andrzej N wrote:
> Short question. In genome I'm working now there are long repeats (~5 kbp)
> multiple times. How to make MIRA distribute that sequences from "within"
> that region equal, instead collect them in one place, with like 200x
> coverage? Uniform read distribution is not doing it :(. 454 data, one end,
> coverage about 20x.
What you are describing only affects contigs made of repeats longer than a
read length (or than the insert size of paired reads).
In the past, MIRA indeed made multiple copies of repeats and stored them
separately ... because I too feel that this is the right approach.
Until people complained that those version of MIRA were bad program because
they made "much more" contigs than other assemblers. When I then started to
see assembler comparisons involving MIRA just based on N50 and number of
contigs, I mailed the authors of some to point out the important difference. I
either got no response, or responses from people I had then to assume were
undergrad students who had no idea about the underlying problematic and had
this as a "homework" or response from people with enough knowledge but told me
that the "needed something easy to measure and they had no time for more in-
depth analysis of the assembly quality".
I then grudgingly reverted my decision and made MIRA again collapse repetitive
contigs.
Sad, but true.
> I hope MIRA is not deleting that repeats. How to keep them together with my
> other contigs?
Erm, what do you mean by that?
B.
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