<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Both transcript and protein evidence will go into the AED calculation for overlap support. So in both cases the chosen model had better overlap (protein evidence will not count toward the eAED overlap calculation if it is out of frame with the model it is supposed to be supporting). The larger merged model generates a clutering affect on it’s evidence, so it’s evidence set for AED calculation is slightly different than the SNAP and Augustus model would generate. In both cases, I think GeneMark is hurting more than it is helping. You may want to just drop it from the analysis (unless it’s a fungi, I often find GeneMark can have that affect).<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 12, 2017, at 12:09 AM, Xabier Vázquez-Campos <<a href="mailto:xvazquezc@gmail.com" class="">xvazquezc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi there,<br class=""><br class=""></div>I was visualising the annotations and I realised that in some cases, what it seems to be a gene is splitted according to one of the gene models, despite that the other 2, est2genome and prot2genome suggest that it isn't the case.<br class=""><div class=""><br class=""><span id="cid:ii_j8o0g4b70_15f0f021abda3b14"><split-gene.png></span><br class=""><br class=""></div><div class="">Although the opposite also happens.<br class=""></div><div class=""><br class=""><span id="cid:ii_j8o0g4bw1_15f0f021abda3b14"><merged-gene.png></span><br class=""></div><div class="">For some reason, the "out of place" model is always (or almost) the one from Genemark.</div><div class=""><br class=""></div><div class="">How much weight does carry the RNAseq and protein data on this decision (if any)?</div><div class="">How exactly is the final gene selected?</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Xabi<br class=""></div><div class=""><div class=""><br class="">-- <br class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">Xabier Vázquez-Campos, <i class="">PhD</i><br class=""><i class="">Research Associate</i><br class="">NSW Systems Biology Initiative<br class="">School of Biotechnology and Biomolecular Sciences<br class="">
The University of New South Wales<br class="">Sydney NSW 2052 AUSTRALIA<br class=""></div></div></div></div></div></div></div></div></div></div></div>
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