Re: [Cg-pipeline-users] prediction question

[Lee K. <ls...@gm...>]

Thank you for pointing that out.  I might not have caught that on my own.
 I added the linker sequence so that BLAST results would be more accurate
but didn't think about how it might affect GeneMark or Glimmer.  I need to
find a happy medium, but in the meantime, CGP v0.3 does not have this
linker and you can try that for now.

Also, but untested, is that you can alter this line so that the linker is
an empty string in run_prediction

$$settings{assembly_linker} ||= "NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN";



On Tue, Jul 16, 2013 at 4:20 AM, kokwei <kok...@gm...> wrote:

>
> Hello,
>
> I notice that for cg pipeline, assembly linker used for joining the
> contigs/scaffolds during prediction is included in the gene model
> instead of just forming as a linker (I found VXX as 5' and XXHT as 3' of
> some gene models). All the coordinates of gene models also have an
> offset of 36 bp due to the inclusion of the linker at the 5' end of the
> assembly sequence.
> Is it possible to remove those linker from the gene model during
> pipeline execution and output correct location? Thanks.
>
>
>
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-- 
Lee Katz, Ph.D.