[apollo] 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):

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

[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
<http://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

Post by 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): http://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
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[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

Post by 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
<http://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

Post by 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): http://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
| 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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
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[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

Post by Rob Syme
Hi Deepak
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
https://gist.github.com/robsyme/dc2fd2c211bbb5f6803919d858113471
-r

Post by 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
<http://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

Post by 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
http://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
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
| 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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.