<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="">The previous linked comment explains in detail —> <a href="https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ" class="">https://groups.google.com/<wbr class="">forum/#!msg/maker-devel/<wbr class="">wtmNRtRa-ko/iC4KTuIitGEJ</a><div class=""><br class=""></div><div class="">Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Thank you all. Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?<br class=""><br class=""></div>The default maker2 gene set includes all genes with AED less than 1. Do you think eAED is a better choice to filter gene models than AED? <br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""><div class=""><div class=""><br class=""><div class=""> <br class=""></div></div></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-10-04 18:39 GMT-04:00 Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">This one is an even better explanation than the answer I just gave. Thank you.<span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class="h5"><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <<a href="mailto:xvazquezc@gmail.com" target="_blank" class="">xvazquezc@gmail.com</a>> wrote:</div><br class="m_2206316325980755148Apple-interchange-newline"><div class=""><div dir="ltr" class="">Carson commented on this here<br class=""><a href="https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ" target="_blank" class="">https://groups.google.com/<wbr class="">forum/#!msg/maker-devel/<wbr class="">wtmNRtRa-ko/iC4KTuIitGEJ</a><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 5 October 2017 at 09:31, Quanwei Zhang <span dir="ltr" class=""><<a href="mailto:qwzhang0601@gmail.com" target="_blank" class="">qwzhang0601@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="">Hello:<br class=""><br class=""></div>I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. <br class=""><br class="">Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? <br class=""><div class=""><div class=""><br class="">>maker-Contig2656-snap-gene-26<wbr class="">9.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35<br class=""></div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class="">Best</div><span class="m_2206316325980755148HOEnZb"><font color="#888888" class=""><div class="">Quanwei<br class=""></div></font></span></div></div>
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