ORF finder used in Apollo

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ORF finder used in Apollo

Surya Saha-2
Hi Nathan,

What is the script/tool in Web Apollo that finds the open reading frame when a annotator pulls a gene model from a track into the user created annotations pane? I have a bunch of models mapped on a genome using GMAP but I'm not happy with the ORF calls as they are missing start/stop codons etc. I get much better ORF calls in Apollo when I load the GFF for the mapped models as a track and create a new annotation manually by dragging up the mapped model. 

I was wondering if I could run this ORF finder tool on the command line on a few thousand models mapped by GMAP.

Please let me know if my question is not clear. Thanks and Cheers!

-Surya


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Re: ORF finder used in Apollo

nathandunn

Surya,

The ORF finder is part of Apollo and not really done as a separate library.

That being said, it sounds like maybe you want to use a gff loader script to have apollo automatically create annotations for you based on existing gene models. 



I hope this answers your question, but let me know if not. 
  

Nathan


On Aug 4, 2020, at 9:03 AM, Surya Saha <[hidden email]> wrote:

Hi Nathan,

What is the script/tool in Web Apollo that finds the open reading frame when a annotator pulls a gene model from a track into the user created annotations pane? I have a bunch of models mapped on a genome using GMAP but I'm not happy with the ORF calls as they are missing start/stop codons etc. I get much better ORF calls in Apollo when I load the GFF for the mapped models as a track and create a new annotation manually by dragging up the mapped model. 

I was wondering if I could run this ORF finder tool on the command line on a few thousand models mapped by GMAP.

Please let me know if my question is not clear. Thanks and Cheers!

-Surya



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Re: ORF finder used in Apollo

Surya Saha-2
Hi Nathan,

Thank you for the quick response! This might do the trick. I might try the perl script first because I'm old :) 

Does it do anything different than the load_gff in the python-apollo project?

Cheers,
Surya


On Tue, Aug 4, 2020 at 12:40 PM Nathan Dunn <[hidden email]> wrote:

Surya,

The ORF finder is part of Apollo and not really done as a separate library.

That being said, it sounds like maybe you want to use a gff loader script to have apollo automatically create annotations for you based on existing gene models. 



I hope this answers your question, but let me know if not. 
  

Nathan


On Aug 4, 2020, at 9:03 AM, Surya Saha <[hidden email]> wrote:

Hi Nathan,

What is the script/tool in Web Apollo that finds the open reading frame when a annotator pulls a gene model from a track into the user created annotations pane? I have a bunch of models mapped on a genome using GMAP but I'm not happy with the ORF calls as they are missing start/stop codons etc. I get much better ORF calls in Apollo when I load the GFF for the mapped models as a track and create a new annotation manually by dragging up the mapped model. 

I was wondering if I could run this ORF finder tool on the command line on a few thousand models mapped by GMAP.

Please let me know if my question is not clear. Thanks and Cheers!

-Surya



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Re: ORF finder used in Apollo

nathandunn

The perl script has been tested over the last decade, so it might be more reliable, but *knock on wood* they should give equivalent results. 

Nathan


On Aug 4, 2020, at 11:01 AM, Surya Saha <[hidden email]> wrote:

Hi Nathan,

Thank you for the quick response! This might do the trick. I might try the perl script first because I'm old :) 

Does it do anything different than the load_gff in the python-apollo project?

Cheers,
Surya


On Tue, Aug 4, 2020 at 12:40 PM Nathan Dunn <[hidden email]> wrote:

Surya,

The ORF finder is part of Apollo and not really done as a separate library.

That being said, it sounds like maybe you want to use a gff loader script to have apollo automatically create annotations for you based on existing gene models. 



I hope this answers your question, but let me know if not. 
  

Nathan


On Aug 4, 2020, at 9:03 AM, Surya Saha <[hidden email]> wrote:

Hi Nathan,

What is the script/tool in Web Apollo that finds the open reading frame when a annotator pulls a gene model from a track into the user created annotations pane? I have a bunch of models mapped on a genome using GMAP but I'm not happy with the ORF calls as they are missing start/stop codons etc. I get much better ORF calls in Apollo when I load the GFF for the mapped models as a track and create a new annotation manually by dragging up the mapped model. 

I was wondering if I could run this ORF finder tool on the command line on a few thousand models mapped by GMAP.

Please let me know if my question is not clear. Thanks and Cheers!

-Surya




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