[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

[Carson Holt]

The maker_map_ids script that comes with MAKER can be used to generate new names of the style PREFIX###### or PREFIX_######.  You can use the --sort_order flag to sort the contigs in whatever your preferred order is before generating the new names.

Then use the map_gff_ids  and map_fasta_ids to change the names in the gff3 and fasta files respectively.

Here is some extra information from a tutorial where the maker_map_ids script is used --> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Post_Processing_of_Annotations

--Carson

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[Guohong Cai]

Great！－－－Guohong