[mira_talk] Re: Problem with Paired 454, MP Illumina, MIRA and Bambus

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sat, 9 Jul 2011 10:39:45 +0200

On Jul 6, 2011, at 23:19 , Nestor Zaburannyi wrote:
> I have 454 paired data and Illumina Mate-Pair data. It took me some time to 
> figure out that not the Bambus is wrong... Long story short:

Actually I am not so sure that Bambus is correct :-)

One thing to keep in mind are the orientation of the pairs and what the 
scaffolder expects:
- Sanger pairs are oriented like this:   ------>    <--------  and that is what 
Bambus wants per default
- 454 pairs are originally oriented like this:  -------->    --------->   but 
as scaffolders (and MIRA) originally did not expect that, I use a trick by 
letting sff_extract reverse one sequence so that everything as back to 
"normal". Nowadays MIRA could also use the forward / forward orientation, but I 
had not time to change sff_extract.
- Illumina paired-end reads look like this:    -------->   <---------  ... 
which makes it easy.
- Illumina mate-pairs look like this:    <---------    ---------->    ... which 
again lets scaffolders like Bambus despair as the expect something different. 
MIRA does not care there, it can work with that, too.

> Most of the contigs are not joined properly and we get hundreds of thousands 
> "Invalid" links with consistent distance between them. Something like:

Which is a symptom of what I described: mate-pairs are facing outwards, Bambus 
expects them to face inwards.

There is no easy solution to this, the simplest one I can think of is to 
reverse all reads of the Illumina mate-pair set (both sets!) and then assemble. 
Should keep Bambus happy.

Hope that helps,
  Bastien



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