map_forward=1 not mapping reference ID's to output correctly

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map_forward=1 not mapping reference ID's to output correctly

kapeel

Hi,

I am trying to update community annotation in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.

Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR 34129 gene 47121 mRNA 53708 three_prime_UTR
MAKER gene count->  
awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105

In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
. So not sure why we dont have the all the community gene models mapped in the MAKER output

Thanks

Kapeel
--

Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/


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Re: [CAUTION: Suspicious Link] map_forward=1 not mapping reference ID's to output correctly

Poelchau, Monica

Hi Kapeel,

 

If you just want your community annotations to replace models in an existing gene set, we have a tool for this:

 

https://github.com/NAL-i5K/GFF3toolkit

 

You’d need to run gff3_QC on your annotation files first to make sure your annotations are okay, then use gff3_merge to merge your community annotations with your existing gene set (in gff3 format). If you end up trying this out - we’re actively developing the GFF3toolkit, so feel free to post an issue if you notice any problems.

 

Hth,

 

Monica

 

From: maker-devel <[hidden email]> on behalf of Kapeel Chougule <[hidden email]>
Date: Friday, June 22, 2018 at 13:53
To: "[hidden email]" <[hidden email]>
Subject: [CAUTION: Suspicious Link][maker-devel] map_forward=1 not mapping reference ID's to output correctly

 

PROCEED WITH CAUTION: This message triggered warnings of potentially malicious web content. Evaluate this email by considering whether you are expecting the message, along with inspection for suspicious links.

Questions: [hidden email]


Hi,

 

I am trying to update community annotation in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.



Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR 34129 gene 47121 mRNA 53708 three_prime_UTR

MAKER gene count->  

awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105

 

In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
. So not sure why we dont have the all the community gene models mapped in the MAKER output

Thanks

Kapeel
--

 

Kapeel Chougule

Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/





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Re: [CAUTION: Suspicious Link] map_forward=1 not mapping reference ID's to output correctly

Carson Holt-2
A quick overview of MAKER behavior. MAKER will keep everything in model_gff as long as you don’t provide another predictor to run or pred_gff file to use. But if you give it a predictor to run, it takes that as an indicator that you want to update models. So model_gff may get replaced by another prediction that overlaps it but scores better.

So depending on the behavior you want, make sure you are using model_gff and do or don’t provide a gene predictor to run.

—Carson



On Jun 22, 2018, at 2:04 PM, Poelchau, Monica <[hidden email]> wrote:

Hi Kapeel,
 
If you just want your community annotations to replace models in an existing gene set, we have a tool for this:
 
 
You’d need to run gff3_QC on your annotation files first to make sure your annotations are okay, then use gff3_merge to merge your community annotations with your existing gene set (in gff3 format). If you end up trying this out - we’re actively developing the GFF3toolkit, so feel free to post an issue if you notice any problems.
 
Hth,
 
Monica 
 
From: maker-devel <[hidden email]> on behalf of Kapeel Chougule <[hidden email]>
Date: Friday, June 22, 2018 at 13:53
To: "[hidden email]" <[hidden email]>
Subject: [CAUTION: Suspicious Link][maker-devel] map_forward=1 not mapping reference ID's to output correctly
 

PROCEED WITH CAUTION: This message triggered warnings of potentially malicious web content. Evaluate this email by considering whether you are expecting the message, along with inspection for suspicious links.

Questions: [hidden email]


Hi,
 
I am trying to update community annotation in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.


Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR 34129 gene 47121 mRNA 53708 three_prime_UTR
MAKER gene count->  
awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105
 
In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
. So not sure why we dont have the all the community gene models mapped in the MAKER output

Thanks

Kapeel
-- 
 
Kapeel Chougule

Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. _______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
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