Re: [Cg-pipeline-users] prediction question

[Jay H. <jhu...@gm...>]

Hi Kok,
Lee means he modified the source code in the script run_prediction, so 
you can download this version here: 
http://sourceforge.net/p/cg-pipeline/code/583/tree/cg_pipeline/branches/lkatz/scripts/run_prediction
-Jay

On 8/1/2013 4:15 AM, kok wrote:
> 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.
>>>>
>>>>
>>>>             ------------------------------------------------------------------------------
>>>>             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...
>>>>             <mailto:Cg-...@li...>
>>>>             https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users
>>>>
>>>>
>>>>
>>>>
>>>>         -- 
>>>>         Lee Katz, Ph.D.
>>>
>>>
>>>
>>>
>>>     -- 
>>>     Lee Katz, Ph.D.
>>
>>
>>
>>
>> -- 
>> Lee Katz, Ph.D.
>
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> Cg-pipeline-users mailing list
> Cg-...@li...
> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users