[maker-devel] maker gene order in gff output

[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_G
MOD_Online_Training_2014#Post_Processing_of_Annotations

--Carson


From:  Guohong Cai <caigh02 at gmail.com>
Date:  Thursday, May 29, 2014 at 1:15 PM
To:  "<maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker gene order in gff output

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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