[mira_talk] Re: Multiple long repeats in genome.
- From: Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 20 Mar 2011 10:02:56 -0400
Dear Bastien,
I feel that you should change MIRA back to the old behavior which
you thought was the right approach. In this case, can you make the
behavior controllable by an option?
I use MIRA instead of other programs largely because I trust that
you have done the "right" things in the implementation and because the
results have been good.
Thanks. --Bob
Bastien Chevreux wrote:
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.
begin:vcard
fn:Robert Bruccoleri
n:Bruccoleri;Robert
org:Audacious Energy, LLC and Congenomics, LLC
adr:;;;;;;USA
email;internet:bruc@xxxxxxx
title:President
version:2.1
end:vcard
Other related posts:
