[mira_talk] Re: MIRA: I am doing it wrong.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 10 Dec 2009 19:15:05 +0100
On Mittwoch 09 Dezember 2009 Alessandro Riccombeni wrote:
> Sorry for being dumb. Yes, I just checked the Titanium adaptor and its
> reverse complement and they are both present in my reads.
Ummmm, adaptors are not the problem, these are masked by the Roche software
(well, 99.9% of the time). What's important are the paired-end linkers, and
Titanium uses _two_ of them (GS20 and FLX protocols used only one).
Can you please try the following: download 'sff_extract' in
http://www.chevreux.org/tmp/mira_3rdparty_10-12-2009.tar.bz2
Then follow the walkthrough "Extracting paired-end data from SFF" in the 454
usage manual of MIRA (currently it's
http://mira-assembler.sourceforge.net/docs/mira_454.html#section_28
Can you then please report back whether this fixes your problem?
Regards,
Bastien
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