Re: [Cg-pipeline-users] prediction question

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

Hi Jay,

Thanks for pointing me to the location, didn't notice about the 
existence of the page before.


On 1/8/2013 10:22 AM, Jay Humphrey wrote:
> 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
>