Building eukaryotic rrna operon database

[DeniRibicic]

Hi,

I am in a process of trying to build up an eukaryotic full rrna operon database in order to be able to use it with long amplicon ONT generated sequences. The idea is to use the ncbi reference eukaryotic representative genomes database (ref_euk_rep_genomes) and extract rrna parts using barrnap. In order to do so, and to retrieve rrna operons of expected size, would the argument --reject do the work here? Say I am expecting size of ca. 4500 bp, and use --reject on 3000 bp, everything below this size length will be filtered out?

Also, I'd appreciate any comments or suggestions on how you would do this, or is this a valid approach at all?

Thanks