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Hi Felipe,
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<div>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. </div>
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<div>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. </div>
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<div>~Daniel</div>
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<div><span style="font-family: Tahoma; font-size: small; ">Daniel Ence</span></div>
<div><span style="font-family: Tahoma; font-size: small; ">Graduate Student</span></div>
<div><a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Eccles Institute of Human Genetics</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">University of Utah</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">15 North 2030 East, Room 2100</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Salt Lake City, UT 84112-5330</span></div>
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<div>On May 22, 2014, at 10:13 PM, Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu">fbarreto@ucsd.edu</a>></div>
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<div dir="ltr">Hi, all,
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<div>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. </div>
<div>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.
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<div>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?</div>
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<div>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? </div>
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<div>Thanks for any help. I can see the light at the end of the tunnel!</div>
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<div>Felipe</div>
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-- <br>
Felipe Barreto<br>
Post-doctoral Scholar<br>
Scripps Institution of Oceanography<br>
University of California, San Diego<br>
La Jolla, CA 92093 </div>
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