I knew there was a reason why you are the one writing the software and I'm the one asking the questions ;-)
seriously the mira --> bambus--> mira is as simple as clever, thanks. I tried it and I realized I have 3 other problems.For all questions please consider I have an excess of reads so we can be very strict.
1 Repeats: could you please tell me what nnr would you set in this situation?
0 8200338 1 1253412 2 168676 3 30776 4 6770 5 3196 6 2272 7 2074 8 1538 9 568 10 476 11 208 12 338 13 306 14 318 15 258 16 210 17 166 18 212 19 196 20 200 21 198 22 234 23 152 24 100 25 72 26 28 27 26 28 32 29 42 30 44 31 32 32 42 33 54 34 68 35 32 36 64 37 86 38 40 39 78 40 68 41 50 42 56 43 48 44 50 45 48 46 26 47 46 48 32 49 30 50 22 51 12 52 4 56 2 57 62 sequencing errors: you said that having more zeros than 1s is bad, so in my situation what should I do? jump off a cliff? change sequence company?
0 8200338 1 12534123 chimeras: I remember in a previous version that after the annoying request of some italian guy (me) you implemented a chimera finder. it found around 4000 in my assembly. Is it possible to set some parameter to make this search less lenient. I'm willing to lose some good reads in order to get read of chimeras
Always thankful Davide
On Montag 07 September 2009 Davide Sassera wrote:What do you guys do? you take the Bambus output as "right" as it is or you have a method to check the quality and possibly modify the scaffold?I never worked with Bambus but had some scripts cobbled together which failed doing things automatically more often than not ... but with some manual help I always got my scaffolds.What I did then was this: take the scaffold as backbone and perform a mapping assembly on it. With that, go into gap4 and looked for the last remaining uncertainties.I think you shoud be able to do this also with the Bambus scaffold. Hope this helps, Bastien
-- Davide Sassera Sezione di Patologia Generale e ParassitologiaDipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria Facoltà di Veterinaria
Università degli Studi di Milano Via Celoria 10, 20133, Milano, ITALY Tel: +39 0250318094 Fax: +39 0250318095
