Bulk loading GFF3 has no CDS features

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Bulk loading GFF3 has no CDS features

Rob Syme
I've tried to bulk-load a gff3 file into apollo, but the resulting genes have no CDS features. I can force the CDS to be written by using the "Select longest ORF" for each gene individually, but that is not really feasible for every gene in the genome.

Here is an example (the password you see is just a junk password, and the apollo instance is not live on the web): https://youtu.be/k01YaNa9L68
Version: 2.0.4-RC2
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.7.0_101

Am I doing something wrong?

Thanks!

-r




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: Bulk loading GFF3 has no CDS features

Deepak Unni
Hi Rob,

Thank you for the video as it made it easy to identify the problem. 
It looks like the addFeature method is being called, instead of addTranscript.

Can you try loading again, but this time ignore the -d and -D arguments.

Also, are you using the add_transcripts_from_gff3_to_annotations.pl script that is part of Apollo 2.0.4 RC2?

It would be great if you can share you GFF3 so that I can test it here locally as well.

Cheers,

Deepak



On Wed, Jul 27, 2016 at 5:16 AM, Rob Syme <[hidden email]> wrote:
I've tried to bulk-load a gff3 file into apollo, but the resulting genes have no CDS features. I can force the CDS to be written by using the "Select longest ORF" for each gene individually, but that is not really feasible for every gene in the genome.

Here is an example (the password you see is just a junk password, and the apollo instance is not live on the web): https://youtu.be/k01YaNa9L68
Version: 2.0.4-RC2
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.7.0_101

Am I doing something wrong?

Thanks!

-r




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: Bulk loading GFF3 has no CDS features

Rob Syme
Hi Deepak

I think I was doing two things wrong:
1) I hadn't checked out the 2.0.4 RC2 tag
2) I included the -d and -D arguments. 

The bulk loading works a charm now. Thanks! If you still want the gff3 I was using, you can find a copy here: https://gist.github.com/robsyme/dc2fd2c211bbb5f6803919d858113471

-r

On Wed, 27 Jul 2016 at 22:57 Deepak Unni <[hidden email]> wrote:
Hi Rob,

Thank you for the video as it made it easy to identify the problem. 
It looks like the addFeature method is being called, instead of addTranscript.

Can you try loading again, but this time ignore the -d and -D arguments.

Also, are you using the add_transcripts_from_gff3_to_annotations.pl script that is part of Apollo 2.0.4 RC2?

It would be great if you can share you GFF3 so that I can test it here locally as well.

Cheers,

Deepak



On Wed, Jul 27, 2016 at 5:16 AM, Rob Syme <[hidden email]> wrote:
I've tried to bulk-load a gff3 file into apollo, but the resulting genes have no CDS features. I can force the CDS to be written by using the "Select longest ORF" for each gene individually, but that is not really feasible for every gene in the genome.

Here is an example (the password you see is just a junk password, and the apollo instance is not live on the web): https://youtu.be/k01YaNa9L68
Version: 2.0.4-RC2
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.7.0_101

Am I doing something wrong?

Thanks!

-r




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: Bulk loading GFF3 has no CDS features

Deepak Unni
Hi Rob,

Glad to hear that it works. 
I tested the bulk load script with your GFF3 and I can confirm that it works on my end as well.

Thanks for checking with us.

Cheers,

Deepak

On Wed, Jul 27, 2016 at 9:55 PM, Rob Syme <[hidden email]> wrote:
Hi Deepak

I think I was doing two things wrong:
1) I hadn't checked out the 2.0.4 RC2 tag
2) I included the -d and -D arguments. 

The bulk loading works a charm now. Thanks! If you still want the gff3 I was using, you can find a copy here: https://gist.github.com/robsyme/dc2fd2c211bbb5f6803919d858113471

-r

On Wed, 27 Jul 2016 at 22:57 Deepak Unni <[hidden email]> wrote:
Hi Rob,

Thank you for the video as it made it easy to identify the problem. 
It looks like the addFeature method is being called, instead of addTranscript.

Can you try loading again, but this time ignore the -d and -D arguments.

Also, are you using the add_transcripts_from_gff3_to_annotations.pl script that is part of Apollo 2.0.4 RC2?

It would be great if you can share you GFF3 so that I can test it here locally as well.

Cheers,

Deepak



On Wed, Jul 27, 2016 at 5:16 AM, Rob Syme <[hidden email]> wrote:
I've tried to bulk-load a gff3 file into apollo, but the resulting genes have no CDS features. I can force the CDS to be written by using the "Select longest ORF" for each gene individually, but that is not really feasible for every gene in the genome.

Here is an example (the password you see is just a junk password, and the apollo instance is not live on the web): https://youtu.be/k01YaNa9L68
Version: 2.0.4-RC2
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.7.0_101

Am I doing something wrong?

Thanks!

-r




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.