[maker-devel] Alternative splicing options

[Felipe Barreto]

Hey guys,

Great to hear!!  I will be anxious to try it out.  Thanks for your prompt
help!

Cheers,

Felipe


On Fri, May 23, 2014 at 8:07 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I'd like to add that alternate splice forms will be generated off of the
> mutually exclusive EST evidence, so how well it performs as well as whether
> or not it can even generates other splice forms will depend entirely on the
> quality of your EST evidence.
>
> --Carson
>
>
> From: Daniel Ence <dence at genetics.utah.edu>
> Date: Friday, May 23, 2014 at 8:55 AM
> To: Felipe Barreto <fbarreto at ucsd.edu>
> Cc: MAKER group <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Alternative splicing options
>
> Hi Felipe,
>
> The alternative splice option is full-developed and functional option in
> MAKER. What it does is tell MAKER to consider gene models with mutually
> exclusive evidence. For example, if there are two models at a locus and
> evidence that supports one exon in one model and a different exon in
> another model, both those models might make it into the final geneset.
>
> From the workflow you described, I think you'd have to redo only the
> fourth and final round of MAKER annotation. As a general principle for
> trying out new options on your annotations, I'd recommend choosing a big
> scaffold, running it with alt_splice=1, and seeing how you like the
> results.
>
> ~Daniel
>
>
>
> Daniel Ence
> Graduate Student
> dence at genetics.utah.edu
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> On May 22, 2014, at 10:13 PM, Felipe Barreto <fbarreto at ucsd.edu>
>  wrote:
>
> Hi, all,
>
> I just finished a fourth and final iterative round with Maker, training
> predictors in between, and I am very happy with the results.  What I would
> like to try now is to annotate alternative splicing variants, and I know
> the ctrl file has the alt_splice option.
> However, I am intrigued by the lack of information regarding this option.
>  I could not find many discussions in this group, and most genome
> publications using Maker are unclear about whether they annotated
> alternative transcrips, so my guess is they didn't.
> So I was wondering whether there is a reason for that.  Is that function
> not well developed in Maker?  Should I stay away from it?
>
> Assuming it is OK to give it a try (provided I don't get discouraged
> here), what is the best approach to take, considering I already obtained
> what I considered is a solid set of gene models after four rounds of
> annotation?  Should I start over by turning on alt_splice, and training
> gene predictors from those outputs?  Or would it be appropriate to simply
> repeat my latest round, changing only alt_splice=1?
>
>
> Thanks for any help.  I can see the light at the end of the tunnel!
>
> Felipe
>
> --
> Felipe Barreto
> Post-doctoral Scholar
> Scripps Institution of Oceanography
> University of California, San Diego
> La Jolla, CA 92093
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-- 
Felipe Barreto
Post-doctoral Scholar
Scripps Institution of Oceanography
University of California, San Diego
La Jolla, CA 92093
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