[mira_talk] Re: Vector screen

  • From: Leonor Palmeira <mlpalmeira@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 15 Mar 2011 11:15:01 +0100

On 15/03/11 10:57, Tony Travis wrote:

On 14/03/11 22:57, Bastien Chevreux wrote:

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.

Just wondering here ...


Hi, Bastien.

What about people who do whole BAC sequencing?

We are using MIRA just now to assemble SSAHA2 screened 454 and Solexa
reads from whole BAC shotgun sequencing. Other people I know have also
sequenced whole BAC's instead of excising the BAC insert to sequence.
Well, from my own point of view, for a whole BAC 454 sequencing, I prefer to assemble the sequence containing the BAC as a whole, and then excise the BAC from the assembly. This allows me to make sure the assembly ran well, including around the BAC. I don't see the necessity for vector clipping the reads in this particular case. 

Leonor.



Bye,

Tony.


--
Leonor Palmeira, PhD

Phone: +32 4 366 42 69
Email: mlpalmeira AT ulg DOT ac DOT be
http://sites.google.com/site/leonorpalmeira

Immunology-Vaccinology, Bat. B43b
Faculty of Veterinary Medicine
Boulevard de Colonster, 20
University of Liege, B-4000 Liege (Sart-Tilman)
Belgium

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