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

[Walenz, B. <bw...@jc...>]

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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