Re: [Cg-pipeline-users] prediction question

[Gmail <kok...@gm...>]

Sure, thanks for reminding.

On 16/07/2013, at 20:54, Lee Katz <ls...@gm...> wrote:

> 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.
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> See everything from the browser to the database with AppDynamics
>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>> Start your free trial of AppDynamics Pro today!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Cg-pipeline-users mailing list
>>>> Cg-...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users
>>> 
>>> 
>>> 
>>> -- 
>>> Lee Katz, Ph.D.
> 
> 
> 
> -- 
> Lee Katz, Ph.D.