Re: [wgs-assembler-users] No Overlaps found

[Thomas H. <tho...@un...>]

Hi,

thanks for the quick reply. I tried a lot, including the fixes from the 
"Known Issues" section. I also did not believe that the pipeline would 
create overlaps between pacBio-pacBio. What got me wondering was that I 
ran into the same error after I removed all but one pacBio read e.g. 
from the PacBio E.coli sample data set and tried to correct this one 
read with the corresponding illumina data set. I also tried all kinds of 
shortRead settings and smaller kmer-sizes and basically the pacbio.spec 
from the sourceforge web site.

For the sample data I used 100bp raw illumina reads (phread+64) and 
2-10kb fragments from contigs of an assembly of these reads, with and 
without artificially introduced indels.

In addition I used a mapper (Shrimp2) to manually map Illumina reads 
onto my sample pacBio reads, which always produced valid mappings. I 
will try again tomorrow - a bit more organized - and log the different 
settings and scenarios to pinpoint the problem.

'til then
thanks
Thomas




Am 23.07.2012 17:31, schrieb Sergey Koren:
> Hi Thomas,
>
> As Brian mentioned, the pipeline will only overlap PacBio to Illumina (or short read data). So the no overlaps error means that no short-reads could be mapped to the PacBio reads and thus no correction can be done. This error is normally caused by either the fastq format output by the 1.3.0 SMRTportal software (which is since fixed in 1.3.1) or by short Illumina data (<64bp). The pacBioToCA wiki page lists suggested solutions to both issues under the Known Issues section:
> https://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Known_Issues
>
> Please let me know if neither one of those suggestions fixes your issue.
>
> Thanks,
> Sergey
> Bioinformatics Scientist
> NBACC
>
> On Jul 23, 2012, at 11:23 AM, Walenz, Brian wrote:
>
>> Hi, Thomas-
>>
>> The pipeline is only looking for overlaps between Illumina and PacBio, not
>> Illumina-to-Illumina or Illumina-to-PacBio.  From the overlaps it builds a
>> consensus sequence representing the PacBio read, and that is the corrected
>> read.
>>
>> Can you describe your data a bit?  How short are the Illumina?  Any changes
>> to parameters for the pipeline?
>>
>> bri
>> --
>> Brian Walenz
>> Senior Software Engineer
>> J. Craig Venter Institute
>>
>> On 7/23/12 10:13 AM, "Thomas Hackl" <tho...@un...> wrote:
>>
>>> Hello,
>>>
>>> I am currently testing the pacBioToCA pipeline on some sample data in
>>> preparation for some upcoming experiments. The pipeline always stopped
>>> with the error: "No Overlaps found". I already figured out that
>>> obviously these overlaps are required within the pacBio read library, or
>>> at least that this solves the issue.
>>>
>>> Since I do not necessarily expect overlaps in our data but still want to
>>> correct them with Illumina short reads for further analysis, I would
>>> like to know, if this is even possible with your pipeline. And also I do
>>> not really understand, why there is an overlap computation step before
>>> the error correction step?
>>>
>>> Regards
>>> Thomas
>>>
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-- 
Thomas Hackl
Julius-Maximilians-Universität
Department of Bioinformatics
97074 Würzburg, Germany
Fon:  +49 931 - 31 86883
Mail: tho...@un...