Quick question:

By looking at your CoverageDistribution.txt file, I can see that there
are numerous low-coverage erroneous k-mers.

I would say that these reads are not Illumina reads and not 454 reads
although I might be wrong.

Therefore, are these color-space reads that you converted to fasta or
fastq using SAET from SOLiD ?


Just asking.

Also, if you happen to work with color space data, do you know a way to
convert color-space contigs into nucleotide-space contigs ?


                       Sébastien

On Mon, 2011-06-20 at 06:59 -0400, Phillip San Miguel wrote:
> 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
> >>> wester...@purdue.edu
> >>>
> >>> 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
> >
> >
> 




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