<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>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.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, May 23, 2014 at 8:55 AM<br><span style="font-weight:bold">To: </span> Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu">fbarreto@ucsd.edu</a>><br><span style="font-weight:bold">Cc: </span> MAKER group <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Alternative splicing options<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi Felipe,
<div><br></div><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><div><br></div><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><div><br></div><div>~Daniel</div><div><br></div><div><br></div><div><br><div apple-content-edited="true"><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></div><br><div><div>On May 22, 2014, at 10:13 PM, Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu">fbarreto@ucsd.edu</a>></div><div> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi, all,
<div><br></div><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.
</div><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><div><br></div><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><div><br></div><div><br></div><div>Thanks for any help. I can see the light at the end of the tunnel!</div><div><br></div><div>Felipe</div><div><div><br></div>
-- <br>
Felipe Barreto<br>
Post-doctoral Scholar<br>
Scripps Institution of Oceanography<br>
University of California, San Diego<br>
La Jolla, CA 92093 </div></div>
_______________________________________________<br>
maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></blockquote></div><br></div></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>