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

  • From: Robin Kramer <kodream@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 21 Jul 2011 14:04:41 -0600

Not really, just look in the perl code and see how it calls bowtie, maybe I
could ask my organization to release the code, but probably not.

Sincerely yours,

Robin

2011/7/21 Juan Daniel Montenegro Cabrera <jdmontenegroc@xxxxxxxxx>

> Dear Robin,
>
> If I undertood correctly, I could use bwa to align the reads to the MIRA
> pre-assembled contigs and then use that alignment and those Contigs to
> scaffold using Sspace, Is that what you meant?
> So, the last release of Sspace accepts bwa alignments?  Is there any
> specific parameter when bwa alignments in sspace?  Do you have any further
> suggestion?
>
> Regards,
>
> Juan Montenegro
> 2011/7/15 Robin Kramer <kodream@xxxxxxxxx>
>
>> We rewrote SSPACE to use bwa.
>>
>>
>> On Fri, Jul 15, 2011 at 10:46 AM, Nestor Zaburannyi <nestor@xxxxxxxxxxxxx
>> > wrote:
>>
>>> Dear Surya,
>>>
>>> > Dear Nestor,
>>>
>>> > I have used them only with Illumina data but I don't recall that they
>>> cannot
>>> > be used with 454 paired reads. Is it explicitly mentioned anywhere?
>>>
>>> In this topic there is mentioning of 454:
>>> http://seqanswers.com/forums/showthread.php?t=8350
>>>
>>> Apart from that, SSPACE is using bowtie with options that exclude any
>>> reads even with one mismatch. And this is hardly the truth for 454.
>>> Especially unclipped, raw data.
>>>
>>>
>>> > In case you are using Velvet, SOPRA can be run in integration with
>>> Velvet
>>> > and the authors suggest that is better than running SOPRA separately
>>> > post-assembly although I have not tried using it this way (yet). Good
>>> luck!
>>>
>>> > -Surya
>>>
>>> > On Fri, Jul 15, 2011 at 12:21 PM, Nestor Zaburannyi <
>>> nestor@xxxxxxxxxxxxx>wrote:
>>>
>>> >> 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
>>>
>>>
>>> >> >> --
>>> >> >> You have received this mail because you are subscribed to the
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>>> please
>>> >> >> visit http://www.chevreux.org/mira_mailinglists.html
>>>
>>>
>>>
>>>
>>> >> --
>>> >> З повагою,
>>> >>  Nestor                            mailto:nestor@xxxxxxxxxxxxx
>>>
>>>
>>> >> --
>>> >> You have received this mail because you are subscribed to the
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>>> >> mailing list. For information on how to subscribe or unsubscribe,
>>> please
>>> >> visit http://www.chevreux.org/mira_mailinglists.html
>>>
>>>
>>>
>>>
>>> --
>>>  З повагою,
>>>  Nestor                            mailto:nestor@xxxxxxxxxxxxx
>>>
>>>
>>> --
>>> You have received this mail because you are subscribed to the mira_talk
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>>>
>>
>>
>

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