[mira_talk] Re: fn in paired-end reads?
- From: Juan Daniel Montenegro Cabrera <jdmontenegroc@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 31 May 2011 16:20:54 -0500
Hello everyone
Regarding this subject, has any of you tried to scaffold the resulting
assembly using the new Bambus package (Bambus 2.0) ? any suggestion on how
to use it with MIRA results? Now we have to build an AMOS bank with all the
data correctly formatted, kind of tricky even using the script goBambus2.py.
I tried to do it but have a problem with mate pair orientation. As I
understand, sff_extract finds the linker removes it and writes 2 sequences,
the first one in normal orientation and the inverse complement of the second
one right?
Well in my final assembly, I can see several mate pairs in different contigs
but cannot join them because mate pairs are in the same orientation instead
of the opposite. But when I reverse-complement on of the contigs, the
distances obtained way off std deviation. What is happening?
Best Regards,
Juan Montenegro
Applied Biotechnology Laboratory
International Potato Center - Lima - Peru
2011/5/31 Bastien Chevreux <bach@xxxxxxxxxxxx>
> On Tuesday 31 May 2011 16:43:47 Cleo HC Ho wrote:
>
> > Thanks a lot! May I ask where you obtain this documention? I couldn't
> find
>
> > it on the sff_extract website.
>
>
> My bad. I wrote the code for the paired-end splitting but somehow missed to
> coordinate with Jose regarding updating the docs.
>
>
> I remember that the question about read naming already came up earlier on
> the talk list and I'd made a note somewhere to take this up, but ... another
> thing I've missed.
>
>
> > Also, why does the reverse read have be written in complement? Aren't the
>
> > right and left sides of the linker from the same strand of DNA?
>
>
> Long story short: when I wrote this, I wanted to test a number of
> assemblers with the data. Those who did not know 454 yet I declared the
> reads to be "Sanger" and with those the algorithms expect to have one
> forward and one reverse read.
>
>
> It also saved me some ten to twenty lines of code in MIRA to teach it that
> some sequencing methods have read pairs in "forward-forward" orientation ...
> which I added a couple of months later anyway.
>
>
>
> Which brings me to: anyone reading this thread who has an oppinion whether
> I should change the default behaviour of sff_extract to not reverse one of
> the reads (and have MIRA also use forward-forward as default expectation in
> 454 paired-ends)?
>
>
> B.
>
>
>
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