[mira_talk] Re: Vector screen
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 15 Mar 2011 08:15:34 +0100
2011/3/14 Bastien Chevreux <bach@xxxxxxxxxxxx>
> On Monday 14 March 2011 21:15:13 Sven Klages wrote:
> > What part of the pre-processing software is capable of vector clipping?
> > You can easily clip 5' adaptors, maybe some basic 3' adaptor clipping,
> but
> > that's it.
> > There is no vector clipping 'module' in the pre-processing pipeline.
>
> Oops, hold on a minute. What I meant is: I never really saw 454 SFF files
> (those created by the Roche software) which had, when done "correctly"[1],
> adaptors left in the unclipped data. Now the quesion I was asking myself is
> why anyone would want to do a "vector" trimming on that data.
>
In some of our bacterial WGS projects we still generate fosmid libraries and
(sanger) fosmid end sequences for
a) scaffolding
b) gap closure
Formerly we did clone-based shotgun libraries of distinct gap-spanning
fosmid clones for gap closure.
We now pool a few gap-spanning fosmids and generate a 454 sequencing
library. That's faster.
That's why we need "real vector clipping"(tm) for this application :-)
>
> Just wondering here ...
>
> > The assembler itself has options to do vector screening and trimming
> prior
> > to the assembly process. But this is not usable outside the assembler
> > suite.
>
> Wasn't that just something added to Newbler to be able to mix 454 and
> Sanger
> (the latter could have vectors)?
>
Yes, but strategies are changing, ... so there may be other purposes as well
:-)
cheers,
Sven
>
> B.
>
> [1] whatever "correctly" is ... I just saw the SFFs as delivered by
> sequencing
> providers and they were "good"
>
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