Hello,
On Sun, 2012-02-05 at 12:35 -0500, Louis Letourneau wrote: > I have 2 libraries one of them is an illumina mate-pair library. > > I ran Ray forcing insert size and got a not-so-bad assembly, but the > scaffold result wasn't so different from the contig result which was > surprising. I wanted to be sure of my distances so I let it guess them. > I was expecting 2 peaks for the mate library, but got none. > > I ploted the attached distribution (attached), and it does identify a > pair peak, but the broad mate distances are not picked up. > Yes, but the R code is the old prototype. > Not the best library, but there clearly is something there. > There is something, I agree. > Is there a way to tell Ray manually that there are 2 distributions in a > library? Can you provide me with the Library1.txt file. I have a test for that and I will fix another reported bug regarding this. The code that does the detection is not actually in plugin_Scaffolder. It is in plugin_Library. plugin_Library/LibraryPeakFinder.cpp You can build a standalone program that takes Library<x>.txt and tells you what it finds. To build it, go in unit-tests and run test_peakFinder.sh Example: [boiseb01@ls30 unit-tests]$ ./peaks ../system-tests/tests/L1-L3/L1-L3/Library0.txt Peak 0 199 19 [boiseb01@ls30 unit-tests]$ ./peaks ../system-tests/tests/L1-L3/L1-L3/Library1.txt Peak 0 9823 1001 [boiseb01@ls30 unit-tests]$ ./peaks ../system-tests/tests/L1-L3/L1-L3/Library2.txt Peak 0 997 99 > > If not, should I only give the mate distribution 4.7k +- 1k That is a possibility, but the plugin_SeedExtender won't see the other one. > or not use > the Ray scaffolder and use something else? > You could try SSPACE, I heard good things. Or possibly the SOAPdenovo scaffolder. > Thanks ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
