[mira_talk] Re: PacBio CCS questions
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 16 Aug 2013 21:50:41 +0200
On Aug 15, 2013, at 1:34 , Matthew D. Pagel <pagel@xxxxxxx> wrote:
> Is there a quick-and-dirty algorithm out there for identifying inversions from
> one subread to the next within a single PB read
I'd have a more pressing, but similar question at the moment: is there a way of
easily identifying reads which for such a FR structure but where the PB
algorithms apparently did not recognise an adapter?
Background: I'm working on the read improvement routines atm and I think that
in the 49 PB reads I took as initial test set (out of >30k from the E.coli
Nature paper), already two reads show such an inversion where there should be
none … ergo it's a sequencing artefact and 4% of reads like this will wreak
havoc with most assembly algorithms. I hate situations like these.
Bonus question: are PB adaptor sequences listed somewhere on the net? The only
place I found some are in the metadata XML files, and they told me
ATCTCTCTCttttcctcctcctccgttgttgttgttGAGAGAGAT
Are there others?
B.
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