[mira_talk] Re: Vector screen
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 Mar 2011 21:15:13 +0100
2011/3/14 Bastien Chevreux <bach@xxxxxxxxxxxx>
> [...]
>
> SSAHA2 and SMALT certainly recognized vector regions in each 454 read
> > sequences. The Mira assembly process was done completely without any
> > error. But the vector sequence were still remained in assembles; Checked
> > by SSAHA2 and BLAST search. The yielded contigs contain the vector
> > sequences at the (one or both) terminal of them and sometimes at the
> > middle of contigs (chimera?).
>
> First thimgs first: is there any special reason why you do a vector screen
> yourself? Normally the 454 pre-processing software is quite good at that
> task
> and the clipping points in the SFF are solid enough ... at least to kmy
> knowledge.
> [...]
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.
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.
cheers,
Sven
Other related posts:
