Using PASA assemblies with MAKER

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Using PASA assemblies with MAKER

Federico López
Hello,

I was wondering what might be the recommended option for using PASA2 alignment assemblies with MAKER3:

1. PASA assemblies in FASTA format (est)
2. PASA assembly structures (est_gff)
3. ORFs from PASA assemblies (protein)

And related to this question, when I use the PASA2 assembly structures in GFF3 format, MAKER reports the error below.

"ERROR: Non-unique top level ID for..."

I suppose all the non-unique IDs need to be renamed for MAKER?

Any help is greatly appreciated.

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Re: Using PASA assemblies with MAKER

Carson Holt-2
MAKER requires the two level match/match_part format. An example of which can be found in the GFF3 specification —> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

I haven’t used PASA, but the file you are providing may be GFF2 or GTF format which is not compatible with GFF3.

—Carson




On Mar 9, 2018, at 9:15 AM, Federico López <[hidden email]> wrote:

Hello,

I was wondering what might be the recommended option for using PASA2 alignment assemblies with MAKER3:

1. PASA assemblies in FASTA format (est)
2. PASA assembly structures (est_gff)
3. ORFs from PASA assemblies (protein)

And related to this question, when I use the PASA2 assembly structures in GFF3 format, MAKER reports the error below.

"ERROR: Non-unique top level ID for..."

I suppose all the non-unique IDs need to be renamed for MAKER?

Any help is greatly appreciated.
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