[maker-devel] maker gene order in gff output

[Guohong Cai]

Great！－－－Guohong


On Thu, May 29, 2014 at 10:11 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
>
> 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
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140530/c3f3968e/attachment-0003.html>