Re: [Cg-pipeline-users] prediction question

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

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...> wrote:

> 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.
>>>
>>>
>>>
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>>
>>
>>
>>  --
>> Lee Katz, Ph.D.
>>
>>
>>
>
>
> --
> Lee Katz, Ph.D.
>
>


-- 
Lee Katz, Ph.D.