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

Dear Bastien,

Thanks for your hints. Indeed, dirty hack involving the reversal of both MP 
read sets helped.

Regards
Nestor

> 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






-- 
З повагою,
 Nestor                            mailto:nestor@xxxxxxxxxxxxx


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