Keeping unsupported predictions

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Keeping unsupported predictions

Khan, Anar
Hi
 
I have very limited EST evidence data, and I’d like to obtain MAKER predictions which aren’t based on EST/protein alignment evidence, as well as those which are. However on setting the “keep_preds” option to 1, the resulting gff file is identical to that obtained with keep_preds=0; on viewing output in GBrowse there seem to be no MAKER calls where ab initio predictions exist and EST/protein matches are lacking. Can someone please let me know the combination of options I need to solicit this behaviour?
 
Thanks in advance!
 
Cheers
Anar
 
 

 


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Re: Keeping unsupported predictions

Carson Hinton Holt
Re: [maker-devel] Keeping unsupported predictions I cannot create the same error.  What version of maker are you using?  Perhaps after knowing which version you are using I can try it again.

Also if you could provide your dataset and maker control files, I can try running exactly as you are.

Thanks,
Carson


On 2/20/11 2:59 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi
 
I have very limited EST evidence data, and I’d like to obtain MAKER predictions which aren’t based on EST/protein alignment evidence, as well as those which are. However on setting the “keep_preds” option to 1, the resulting gff file is identical to that obtained with keep_preds=0; on viewing output in GBrowse there seem to be no MAKER calls where ab initio predictions exist and EST/protein matches are lacking. Can someone please let me know the combination of options I need to solicit this behaviour?
 
Thanks in advance!
 
Cheers
Anar

 
 


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Re: Keeping unsupported predictions

Khan, Anar
Re: [maker-devel] Keeping unsupported predictions

Hi Carson

 

Thanks very much for testing my data. You were correct, upgrading MAKER solved the problem. Hooray!

 

Is MAKER backward compatible, that is, now that I’ve installed 2.09 is it possible to re-run MAKER on existing v2.07 output, to make use of the BLAST/RepeatMasker output files? It seems to work ok on a test data set, just wondering if there might be unseen issues. I’m sorry if this has already been covered on the mailing list or in the documentation and I’ve missed it.

 

Cheers

Anar

 

From: Carson Holt [mailto:[hidden email]]
Sent: Monday, 21 February 2011 4:02 p.m.
To: Khan, Anar; [hidden email]
Subject: Re: [maker-devel] Keeping unsupported predictions

 

I cannot create the same error.  What version of maker are you using?  Perhaps after knowing which version you are using I can try it again.

Also if you could provide your dataset and maker control files, I can try running exactly as you are.

Thanks,
Carson


On 2/20/11 2:59 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi
 
I have very limited EST evidence data, and I’d like to obtain MAKER predictions which aren’t based on EST/protein alignment evidence, as well as those which are. However on setting the “keep_preds” option to 1, the resulting gff file is identical to that obtained with keep_preds=0; on viewing output in GBrowse there seem to be no MAKER calls where ab initio predictions exist and EST/protein matches are lacking. Can someone please let me know the combination of options I need to solicit this behaviour?
 
Thanks in advance!
 
Cheers
Anar

 
 


Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.


 


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Re: Keeping unsupported predictions

Carson Hinton Holt
Re: [maker-devel] Keeping unsupported predictions Any non-compatibility issues should be resolved automatically, that is to say the only issue that may possibly arise is that there might have been a name convention change in how data is archived for certain types, in which case the newer version will ignore old files with different names and just re-run that part of the analysis.

--Carson


On 2/28/11 6:00 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi Carson
 
Thanks very much for testing my data. You were correct, upgrading MAKER solved the problem. Hooray!
 
Is MAKER backward compatible, that is, now that I’ve installed 2.09 is it possible to re-run MAKER on existing v2.07 output, to make use of the BLAST/RepeatMasker output files? It seems to work ok on a test data set, just wondering if there might be unseen issues. I’m sorry if this has already been covered on the mailing list or in the documentation and I’ve missed it.
 
Cheers
Anar
 

From: Carson Holt [[hidden email]]
Sent: Monday, 21 February 2011 4:02 p.m.
To: Khan, Anar; maker-devel@...
Subject: Re: [maker-devel] Keeping unsupported predictions

I cannot create the same error.  What version of maker are you using?  Perhaps after knowing which version you are using I can try it again.

Also if you could provide your dataset and maker control files, I can try running exactly as you are.

Thanks,
Carson


On 2/20/11 2:59 PM, "Khan, Anar" <Anar.Khan@...> wrote:
Hi
 
I have very limited EST evidence data, and I’d like to obtain MAKER predictions which aren’t based on EST/protein alignment evidence, as well as those which are. However on setting the “keep_preds” option to 1, the resulting gff file is identical to that obtained with keep_preds=0; on viewing output in GBrowse there seem to be no MAKER calls where ab initio predictions exist and EST/protein matches are lacking. Can someone please let me know the combination of options I need to solicit this behaviour?
 
Thanks in advance!
 
Cheers
Anar

 
 



Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.






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Re: Keeping unsupported predictions

Khan, Anar
Re: [maker-devel] Keeping unsupported predictions

Brilliant – thanks very much for the info.

 

Cheers

Anar

 

From: Carson Holt [mailto:[hidden email]]
Sent: Tuesday, 1 March 2011 2:06 p.m.
To: Khan, Anar; [hidden email]
Subject: Re: [maker-devel] Keeping unsupported predictions

 

Any non-compatibility issues should be resolved automatically, that is to say the only issue that may possibly arise is that there might have been a name convention change in how data is archived for certain types, in which case the newer version will ignore old files with different names and just re-run that part of the analysis.

--Carson


On 2/28/11 6:00 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi Carson
 
Thanks very much for testing my data. You were correct, upgrading MAKER solved the problem. Hooray!
 
Is MAKER backward compatible, that is, now that I’ve installed 2.09 is it possible to re-run MAKER on existing v2.07 output, to make use of the BLAST/RepeatMasker output files? It seems to work ok on a test data set, just wondering if there might be unseen issues. I’m sorry if this has already been covered on the mailing list or in the documentation and I’ve missed it.
 
Cheers
Anar
 

From: Carson Holt [[hidden email]]
Sent: Monday, 21 February 2011 4:02 p.m.
To: Khan, Anar; maker-devel@...
Subject: Re: [maker-devel] Keeping unsupported predictions

I cannot create the same error.  What version of maker are you using?  Perhaps after knowing which version you are using I can try it again.

Also if you could provide your dataset and maker control files, I can try running exactly as you are.

Thanks,
Carson


On 2/20/11 2:59 PM, "Khan, Anar" <Anar.Khan@...> wrote:
Hi
 
I have very limited EST evidence data, and I’d like to obtain MAKER predictions which aren’t based on EST/protein alignment evidence, as well as those which are. However on setting the “keep_preds” option to 1, the resulting gff file is identical to that obtained with keep_preds=0; on viewing output in GBrowse there seem to be no MAKER calls where ab initio predictions exist and EST/protein matches are lacking. Can someone please let me know the combination of options I need to solicit this behaviour?
 
Thanks in advance!
 
Cheers
Anar

 
 



Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.





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