[maker-devel] Alternative splicing options

[Felipe Barreto]

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

[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

de...@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 <fbar...@ucsd.edu>

 wrote:

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[Carson Holt]

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

[Felipe Barreto]

Hey guys,

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

Cheers,

Felipe

[Fields, Christopher J]

That is exactly what I have seen using this option; genes with very good transcriptome evidence (as one might expect)tend to have more isoforms.  The problem we run into is not having a diverse enough transcriptome set to work with (ours tend to be tissue-specific unfortunately), so we have some genes giving more isoforms than others, but we don’t design the libraries so have no control over it.  We are currently only using Trinity assemblies as input over using TopHat2/Cufflinks.

chris