Hi Sebastien,
They were Illumina 2x100 PE reads. However we did switch to a
higher kmer for that assembly (63, I think.)
We do have a SOLiD, though. SAET doesn't convert color space reads
to sequence space. It examines all the reads to find errors that are
correctable.
Generally to convert a color space sequence to sequence space you
need a "key" base prefixing the sequence.
Phillip
PS The newer SOLiDs -- the 5500XLs have a new chemistry, "ECC", that
will allow direct conversion of the reads to sequence space without loss
of accuracy. But those are just getting installed now.
On 6/22/2011 1:10 PM, Sébastien Boisvert wrote:
> 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
>>>>> [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
>>>
>
>
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