I have been looking at different gff3 to gtf converters, but cannot find a good one that works well for gff3 files downloaded from NCBI Refseq assemblies. I am trying to compare (using the program Eval which only takes in gtf files) an existing refseq annotation with one I created using Maker. Maker provides a script to convert its gff3 output to gtf specifically so that Eval can read it in. This worked great on my Maker output, but did not work for the RefSeq gff file.
I have also used Cufflinks gffread tool with no luck either.
Any help is greatly appreciated!