[maker-devel] Using PASA assemblies with MAKER

[Carson Holt]

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 <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 <flopezo84 at gmail.com> 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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