<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">For AED in general, lower is better, but you have to understand the caveats. With mRNA-seq Nnot all genes may be expressed, not all exons may be captured (mRNA can fold blocking some sequencing reactions), and sometimes the alignment may extend improperly into the intron or even merge into the neighboring gene. Also mRNA-seq captures a lot of things that aren't coding genes. But in general for mRNA-seq, as coverage increases the AED values trend toward 0, and mRNA-seq is the single most informative piece of evidence you can get for annotation (I've seen several very poor genome assemblies with horrible annotations that were saved by mRNA-seq). For mRNa-seq, give MAKER the assembled reads (trinity works well). Also for fungi, the UTR tend to overlap between genes. This can create false merging in the mRNA-seq assemblies (their AED is lower but its a false merge). Use the correct_est_fusion option in the control files to help handle that.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">I know there are also several members of the MAKER mailing list who have extensive experience using mRNA-seq to annotate fungi who may want to add their two cents.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">Thanks,</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><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> Hud Hud <<a href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold">Reply-To: </span> Hud Hud <<a href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 15 April, 2013 11:54 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> maker output<br></div><div><br></div><div><div><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Hi Carson, have a nice day..</div><div>I have a question about the output file from maker, recently i run my longest contigs (100kb) on Maker using rna-seq data from other related species of my genome (same genus)..and ive noticed that i managed to get expressed sequences match annotation compared using just EST and cDNA. Is this due to different size of dataset? as im using larger dataset when im incorporating rna-seq data (assembled transcript combined with cDNA and est) <span style="font-size: 12pt;"> . The value of AED for both prdicted mRNA 0.15 (with rna-seq data) and 0.06(w/o rna-seq data). My question is which one is the most accurate prediction, can i just depends on the value of AED ( the lower the better)? How about the incorporation of rna-seq data in this case,can i conclude that rna-seq improves the annotation
(based on the image i attached). Thanks for your time, really appreciate it.</span></div></div></div></div></span></body></html>