On 9 mars 2014 23:58, David Eccles (gringer) [bioinformat...@gringene.org] wrote: > À : Sébastien Boisvert; denovoassembler-users@lists.sourceforge.net > Objet : Re: RE : [Denovoassembler-users] Coverage Distribution Analysis > guesses coverage peak of 2 instead of 500 > > On 08/03/14 02:44, Sébastien Boisvert wrote: >> The peak coverage reported in this file is not used in the Ray series 2.x.x. >> The peak coverage is instead computed individually for each >> seed. > > Okay, fine, but that is orthogonal to my suggestion about excluding the first > half-peak from coverage calculations. When assembling I get > reports of seeds with coverage of 2 and other seeds with coverage closer to > 500, but would expect a more normal distribution of peak coverage. > > > - David
That's indeed a good point. There are seeds with coverage of 2. Some of these are bubbles and seeds. There is code to eliminate them using their topology, but it is not in production yet. I will review your patch and get back at you. ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
