[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
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