Error while loading PASA generated gff3

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

Error while loading PASA generated gff3

Chougule, Kapeel
Hi,

I am using Apollo version 2.0.8. I get the below error when loading a PASA generated gff3.

"type mRNA is not the same as previous type gene for ID 'ZemaCp026' at /home/kchougul/apollo_install/Apollo-2.0.8/bin/../src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm line 16”

This is how the gene ID looks in the gff3.

Pt      NCBI    gene    47157   47762   .       -       .       ID=ZemaCp026;Name=RPS4
Pt      NCBI    mRNA    47157   47762   .       -       .       ID=ZemaCp026;Parent=ZemaCp026;Name=RPS4
Pt      NCBI    exon    47157   47762   .       -       .       ID=ZemaCp026.exon1;Parent=ZemaCp026
Pt      NCBI    CDS     47157   47762   .       -       0       ID=cds.ZemaCp026;Parent=ZemaCp026

Any recommendation to modify gff.

Thanks

Kapeel





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: Error while loading PASA generated gff3

Sebastien Carrere-2
Dear Kapeel,

Your gene and mRNA share the same ID. This is not valid.

Change gene ID and mRNA Parent to minimize the gff edition.

Sebastien

Le 30 janv. 2019 17:15, "Chougule, Kapeel" <[hidden email]> a écrit :

Hi,

I am using Apollo version 2.0.8. I get the below error when loading a PASA generated gff3.

"type mRNA is not the same as previous type gene for ID 'ZemaCp026' at /home/kchougul/apollo_install/Apollo-2.0.8/bin/../src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm line 16”

This is how the gene ID looks in the gff3.

Pt      NCBI    gene    47157   47762   .       -       .       ID=ZemaCp026;Name=RPS4
Pt      NCBI    mRNA    47157   47762   .       -       .       ID=ZemaCp026;Parent=ZemaCp026;Name=RPS4
Pt      NCBI    exon    47157   47762   .       -       .       ID=ZemaCp026.exon1;Parent=ZemaCp026
Pt      NCBI    CDS     47157   47762   .       -       0       ID=cds.ZemaCp026;Parent=ZemaCp026

Any recommendation to modify gff.

Thanks

Kapeel




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.