[maker-devel] maker gene order in gff output

[Guohong Cai]

Hi Carson,

    In the maker output, the genes have names like  "genemark-scaffold17-
processed-gene-0.0".  Many users probably will eventually give the genes
different names, such as GSGxxx (Genus Species Gene #).

In the gff output, the scaffolds are not in order (either numerical order
or the order of input assembly). On the same scaffold, the genes are not
listed in order either. This will make it a little harder for users to
change the gene IDs. We may name the genes in order from scaffold 1 to
scaffold N, and and each scaffold, order the genes from left to right, e.g
GSG00001, GSG00002). Do you think you can order the genes in the gff
output? For example, order the scaffolds according to the input genome
assembly, and on each scaffold, order the genes from 5' to 3'.

Thanks.

Guohong
Rutgers University
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