Hi Sébastien, Here it is: http://pastebin.com/Mv5ziDVk
Regards, Phillip On 6/17/2011 12:50 PM, Sébastien Boisvert wrote: > What is the content of the CoverageDistribution.txt file with the > smoothing code ? > > > > On Thu, 2011-06-16 at 11:32 -0400, Rick Westerman wrote: >> Sebastian: >> >> Now that I look at the source closer, the version number in the >> v.1.6.1-rc1 link is set to 1.6.0 however the code itself looks like you have >> put in smoothing therefore I am confident that we have the latest and >> greatest. I've recompiled a couple of times, including a time when I >> changed the version number just to be 100% sure that we are running the >> latest code. However our over-all problem of short contigs continues: >> >> The 'LibraryStatistics' file looks like: >> >> ------------------- >> >> File: ../FastQ/000617_TL3360_both.fastq >> NumberOfSequences: 13001302 >> >> Total: 13001302 >> >> NumberOfPairedLibraries: 1 >> >> LibraryNumber: 0 >> InputFormat: Interleaved,Paired >> DetectionType: Automatic >> File: ../FastQ/000617_TL3360_both.fastq >> NumberOfSequences: 13001302 >> AverageOuterDistance: 1018 >> StandardDeviation: 963 >> DetectionFailure: Yes >> >> ------------------- >> >> >> The old file looks like: >> >> ------------------- >> >> File: ../FastQ/000617_TL3360_both.fastq >> NumberOfSequences: 13001302 >> >> Total: 13001302 >> >> NumberOfPairedLibraries: 1 >> >> LibraryNumber: 0 >> InputFormat: Interleaved,Paired >> DetectionType: Automatic >> File: ../FastQ/000617_TL3360_both.fastq >> NumberOfSequences: 13001302 >> AverageOuterDistance: 385 >> StandardDeviation: 628 >> DetectionFailure: Yes >> >> ------------------- >> >> So obviously we are getting a different (and perhaps better) distance >> distribution. >> >> I am going to try some other parameters out but any suggestions would be >> useful >> >> Thanks, >> -- Rick >> >> >> >> ----- Original Message ----- >>> Sebastian: >>> >>> The download link for v1.6.1-rc1 brings up 1.6.0 code. At least that >>> what the version says. We are also still having problems with our >>> sequences. Could you look into this problem. Perhaps create another >>> download? >>> >>> Thanks, >>> >>> -- >>> Rick Westerman >>> [email protected] >>> >>> Bioinformatics specialist at the Genomics Facility. >>> Phone: (765) 494-0505 FAX: (765) 496-7255 >>> Department of Horticulture and Landscape Architecture >>> 625 Agriculture Mall Drive >>> West Lafayette, IN 47907-2010 >>> Physically located in room S049, WSLR building > > ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
