[maker-devel] Mapping gene names

Wed Feb 26 15:50:30 MST 2014

What you can do is run it once with just est_forward=1 and
est2genome/protein2genome set to 1.  Then take those results, pass them in
as model_gff and use the map_forward option to then filter the results based
on mRNA score and that would copy names onto new gene under the standard
MAKER pipeline.  Eventually it’s really supposed to go into a separate tool
that will map genes onto new assemblies (but under the hood the tool will
just be calling MAKER with certain parameters restricted).  I do this
because if people commonly use it mixed with things like SNAP I can start to
get some very weird behaviors.

Thanks,
Carson

From:  Mikael Brandström Durling <mikael.durling at slu.se>
Date:  Wednesday, February 26, 2014 at 3:04 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Mapping gene names

It seems that this could be a very useful option in those cases where you
have firm a priori knowledge of the placement of ESTs. However, while trying
it I note that est_forward implies that the est2genome predictor is turned
on, implicitly. Is this necessary for this to work? I’m after the behavior
you describe below where exonerate is made to try really hard within a
limited region to align an est, but I would not like maker to produce
est2genome predictions.

In general, I think this maker_coor and est_forward is a feature set that is
worthy to be promoted into a documented feature.

THanks,
Mikael

26 feb 2014 kl. 17:09 skrev Carson Holt <carsonhh at gmail.com>:

> It will still work without est_forward.  It just works a little differently.
> Keep in mind this was a hidden feature I used to find stubborn or hard to find
> missing genes after reassembly of a genome.
> 
> If est_forward is provided, MAKER will parse the database to look for the
> maker_coor tags early in the pipeline.  Then it will create a list of
> locations to search, and it will search them even if there are no BLAST
> results to seed the search (normally MAKER gets a BLAST result first and then
> polishes it with exonerate).  So maker_coor=chr1 will cause MAKER to look for
> a match using all of chr1 as the input to exonerate even when BLAST finds
> nothing (this is a very very slow search, but can help pick up one or two
> stubborn genes that don’t remap well).  To allow this, MAKER gives exonerate
> looser matching parameters (i.e. allows for single base pair introns perhaps
> caused by assembly errors).  The logic here is that given the fact that I
> already told MAKER that with some degree of confidence I expect sequence A to
> map to to location X, it will try its hardest to make it match.
> 
> Without est_forward set, the maker_coor= flag still gets read in GI.pm at line
> 1563, but only after a BLAST alignment has already seeded it to the region
> (that BLAST result has the information in its description parameter).  MAKER
> will then ignore seeds completely outside of maker_coor. In addition any BLAST
> seeds that overlap maker_coor will get the search space for alignment
> polishing adjusted to match maker_coor exactly.  Also match parameters for
> exonerate will not be relaxed as they were with est_forward.
> 
> As you can see the behavior, is slightly different (because it’s an accidental
> feature).
> 
> Thanks,
> Carson
> 
> 
> 
> From: Mikael Brandström Durling <mikael.durling at slu.se>
> Date: Wednesday, February 26, 2014 at 6:37 AM
> To: Carson Holt <carsonhh at gmail.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Mapping gene names
> 
> 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>:
> 
>> 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> 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>:
>>> 
>>>> 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>
>>>> Reply-To: Shaun Jackman <sjackman at gmail.com>
>>>> Date: Tuesday, February 25, 2014 at 5:06 PM
>>>> To: <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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> 

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