gff2gff2 --method=sanitize --assembly-report=FILE has wrong default columns as far as I can tell. As far as I can tell the ensembl name is in column 0 and the ucsc name in column 9. Why does gff2gff use column 4 by default? This contains the GenBank-Accn:
This works for human/mouse, because we first copy the content of column 0 to column 4 for lines with "assembled_molecule", but it doesn't work for genomes without assembled molecules.
gff2gff2 --method=sanitize --assembly-report=FILE
has wrong default columns as far as I can tell. As far as I can tell the ensembl name is in column 0 and the ucsc name in column 9. Why does gff2gff use column 4 by default? This contains the GenBank-Accn:This works for human/mouse, because we first copy the content of column 0 to column 4 for lines with "assembled_molecule", but it doesn't work for genomes without assembled molecules.