Re: [Cg-pipeline-users] prediction question

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

Oh, one more thing: remember to clear out project/build/prediction before
running it again, so that it doesn't read from those files.
rm -rf build/prediction/* #but keep the prediction directory there


On Tue, Jul 16, 2013 at 8:46 AM, kokwei <kok...@gm...> wrote:

>  Thanks for your reply.
>
> I understand the needs to add in the assembly linker as it helps to
> truncate the genes at the contig end instead of mistakenly extended into
> previous contig during pseudochromosome generation (I am not sure CGP do
> generate pseudomolecule or not though).
>
> I will try with the empty string to see how it goes and patiently wait for
> better features in CGP v0.5 by you. Thanks!
>
>
> On 16/7/2013 8:16 PM, Lee Katz wrote:
>
> 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.
>
>
>


-- 
Lee Katz, Ph.D.