[mira_talk] Re: Vector screen
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 15 Mar 2011 13:34:10 +0000
On 15/03/11 10:15, Leonor Palmeira wrote:
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.
Hi, Leonor.
The presence of the BAC vector substantially increased the problems we
encountered in assembling the reads. In our case, we have 113 BAC's
sequenced together as a mixture and is important to exclude the BAC
vector from our assembly. In addition, excluding contaminated reads
significally reduced the number of reads included in the assembly.
Bye,
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk
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