[mira_talk] Re: Mira results much worse than newbler
- From: Robin Kramer <kodream@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 14 Jul 2011 15:05:34 -0600
It seems to be able to figure that out on its own, weather from the sff file
or whatever.
It also has some sort of prefix check that will look for other
adapters/primers from the library.
It still misses occasional reverse primers and forward primers.
Sincerely yours,
Robin
On Thu, Jul 14, 2011 at 2:57 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Jul 14, 2011, at 22:38 , Robin Kramer wrote:
> > sff_extract trims of the first however many bases, in the least
> sophisticated way.
> > sffinfo finds the adapters.
>
> Can you please cite a source for that information or perhaps a parameter
> for sffinfo which defines the adaptors which should be used? Or, th best
> possibility, could you show with an example that the extracted sequence from
> sff_extract is different from the one of sffinfo?
>
> The documentation on the SFF file format already defines adaptor clipping
> points in itself ... and those are computed by some Roche pre-processing
> software (and that is certainly not sffinfo) and then written to the SFF. To
> the best of my knowledge, sffinfo just uses that information (as does
> sff_extract).
>
> B.
>
>
>
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