cg-pipeline-users

[Cg-pipeline-users] prediction question

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

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.

Re: [Cg-pipeline-users] prediction question

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

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.

Re: [Cg-pipeline-users] prediction question

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

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.

Re: [Cg-pipeline-users] prediction question

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

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.

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.

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.
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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.
>
>


-- 
Lee Katz, Ph.D.

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.
>>>
>>>
>>>             ------------------------------------------------------------------------------
>>>             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.

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

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
>>
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