[maker-devel] Mapping gene names

[Mikael Brandström Durling]

That might be a useful and time saving accidental feature. But, reading the code, it seems that I need to supply maker_coor but not gene_id, as well as the configuration option est_forward for this to work. Any occurrences of maker_coor in GI.pm seems to be conditioned on set_forward=1 right?

Mikael

26 feb 2014 kl. 14:22 skrev Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>:

Yes.  That should work as well as an accidental feature.

--Carson

Sent from my iPhone

On Feb 26, 2014, at 5:30 AM, Mikael Brandström Durling <mikael.durling at slu.se<mailto:mikael.durling at slu.se>> wrote:

Can this use of maker_coor be used only to hint about the placement of the ests, without affecting the naming of the final genes? Ie if I have a database of EST where I have a priori knowledge of their rough placement, can this placement be given to maker without providing est_forward=1?

Thanks,
Mikael

26 feb 2014 kl. 01:58 skrev Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>:

There is a way.  It’s not a standard option and it’s undocumented, but if you add est_forward=1 to the maker_opts.ctl file, then it will do just that.  The option won’t already be there so you’ll have to type it in.

There is also a feature designed to work with this option.  If you add tags to your fasta headers, those can be used to guide the mapping and naming.  For example, gene_id=<some_gene>  will ensure different isoforms that share a common gene_id get clustered into the same gene, and maker_coor=chr1:1-10000 in the fasta header will force a particular sequence to only be mapped against chr1 within the range of 1-10000 bp  and just using maker_coor=chr1 will force it to only be mapped against chr1.

This is an undocumented way to remap genes onto new assemblies using blast alignments of earlier transcript or protein annotations as a guide.

—Carson




From: Shaun Jackman <sjackman at gmail.com<mailto:sjackman at gmail.com>>
Reply-To: Shaun Jackman <sjackman at gmail.com<mailto:sjackman at gmail.com>>
Date: Tuesday, February 25, 2014 at 5:06 PM
To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: [maker-devel] Mapping gene names


Hi,

I’m annotating a genome using a closely related genome from Genbank, using the .frn (RNA) and .faa (protein) files from Genbank as evidence to annotate my genome. I’ve run Maker, and the annotation seems to have worked well. Is it possible to map the names of the genes from the related species to my annotation? I see the map_forward option, which applies to the model_gff parameter. Is there a similar option for est and protein?

maker_opts.ctl

est=NC_123456.frn
protein=NC_123456.faa
est2genome=1
protein2genome=1


Thanks,
Shaun

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