On Freitag 11 September 2009 Davide Sassera wrote: > 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 6 If MIRA does not complain (MEGAHUBS and such), none. If it complains: try 20. If still complaining: 15, 10, 9, 8, 7, ... > 2 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? Jumping of cliffs higher than 2.57cm is highly discouraged as this might have negative side-effects on the environment in case of blood and gore splashing around. Save the planet, just don't do it :-) Now, things are not always as easy as I write. There are cases when the repeat histogram is not straightforward: - misestimation of the repetitiveness of the data by SKIM. This happens often with highly repetitive genomes (>20%-40%) and always with non-normalised EST. - high-coverage 454 and/or Solexa data To dump the sequence company you'd have to look at the error rate of the reads ion a finsihed project (telling MIRA *not* to use the sequence editor as this would get you away quite a lot of them) > 3 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 Nothing you can do as this is one of the rare algorithms in MIRA where one can't tweak anything at the moment: either there are overlaps spanning reads or not. What you can try is using higher number for -SK:bph, but I doubt that it will lead to any changer. Why do you want to tweak? Do you have the impressions that there are still chimeras? Regards, Bastien -- 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