[mira_talk] Re: Presenting PCR data as paired end reads?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 1 Jul 2010 22:06:21 +0200
On Donnerstag 01 Juli 2010 Sven Klages wrote:
> Hmm, I surely miss something, why not simply:
> [...]
> in the traceinfo XML file? This is a common situation in the finishing
> process
> of a project, that there are more than one read of the same template in the
> same direction (due to failures in sequencing or suboptimal sequence
> quality).
You can do that, but then MIRA will not be able to use the template
information (and complain bitterly about this in the log file).
The reason is pretty dumb: internally MIRA uses read pairs, and the data
structures are not able to cope with more that two reads. I did think at some
time to change this, but I had the impression that the cost/benefit ratio of
implementing these changes simply didn't work out.
Now that we might soon get PacBio data with their strobed reads however I fear
I'll need to revisit that decision (at least for long dark inserts).
> ACK, primer walking from sides generates pairs ... you should probably use
> a different template name for the individual pairs.
Not "probably", but "certainly" :-)
Bastien
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
