[maker-devel] Alternative splicing options

[Daniel Ence]

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<mailto: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<mailto: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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