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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Analysis using refseq complete genome sequence #528

Open frulhuq opened 3 years ago

frulhuq commented 3 years ago

I am running a pan-genome analysis using several Prokka annotated genomes and comparing them to complete genomes in the RefSeq database. The analysis works perfectly, however, in the output file the gene identifier for the reference strain doesn't relate to anything - just looks like a random collection of letters and numbers. I have attached a screenshot of the output file and also of the input files.

I thought that one way to get around it could be to submit the RefSeq sequences into Prokka? But I would like to preserve the original annotations in order to find my favourite genes :)

roary_output contigs_prokka_annotated_file reference_gff_file

EpiDemos82 commented 3 years ago

We are having the same issue with v3.13.0. Were you able to find a solution?