Re: [Cg-pipeline-users] prediction question

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

Just noticing this, sorry I don't quite get the meaning of source 
control here. Is that means you tried removing the assembly linker and 
the prediction run without giving you any problems?

On 22/7/2013 11:56 AM, Lee Katz wrote:
> Hi, just to let you know, I think that this is fixed in the source 
> control now.  I fixed it last week, and so far it hasn't given me any 
> problems.
>
>
> On Tue, Jul 16, 2013 at 11:10 AM, Gmail <kok...@gm... 
> <mailto:kok...@gm...>> wrote:
>
>     Sure, thanks for reminding.
>
>     On 16/07/2013, at 20:54, Lee Katz <ls...@gm...
>     <mailto: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...
>>     <mailto: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...
>>>         <mailto: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.
>
>
>
>
> -- 
> Lee Katz, Ph.D.