Trying to do the same thing, multiple contigs GFF3 file with FASTA included. GFF has only gene/mRNA/exon/CDS calls trying to convert into EMBL. Gets to the export point and then complains that destination format cannot handle keys/qualifiers and then nothing...
Also the Write amino-acids to qualifier - using the GFF3 file writes the translation to the exon features rather than the CDS and then the resulting file is unreadable by artemis. Version 12.0.1 >From the link that Tim posted. Any pointers...would it help to split the fasta+GFFs for each contig ? Many thanks Preethi
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