On October 23, 2014 at 10:25 AM Andrej Benjak <abenjak@xxxxxxxxx> wrote: > To use a gff file as reference in MIRA make sure the nucleotide sequence is > embedded in the file, then it should work. > (most gff files out there, including those from NCBI, don't contain any > sequence) > Albeit if the GFF3 does not have the sequence embedded, you can load it from a separate file (like the data you get from the NCBI). E.g.: readgroup ... data= somefile.fnadata = somefile.gff3 You just need to take care that the sequence file really is the one belonging to the GFF3 file. MIRA can catch a number of mix-up cases, but not all. Therefore, GFF3 with sequence embedded is my recommended approach. B.