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

[Sergey K. <se...@um...>]

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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> 
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