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

Dear Surya,

> Hi Nestor,

> I have had moderate luck with two scaffolders besides the ones already
> mentioned. You might want to try them out.

> SSPACE (
> http://www.baseclear.com/sequencing/data-analysis/bioinformatics-tools/sspace/
> )
> SOPRA (http://www.physics.rutgers.edu/~anirvans/SOPRA/)

> -Surya

Thanks, already gave SSPACE a try. It is good, pity only for short reads as i 
understand. Will also try also SOPRA.


> 2011/7/12 Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>

>> 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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З повагою,
 Nestor                            mailto:nestor@xxxxxxxxxxxxx


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