On 15/03/11 14:34, Tony Travis wrote:
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.
Dear Tony,As already stated by Sven, you are both right for the case of a pool of BACs sequenced together. I was talking of the specific case of a single BAC sequenced as a whole in one library. In this case, I don't vector clip the data.
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 -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html