<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Both est2genome=1 and protein2genome=1 do not predict genes. They simply transfer exonerate alignments which match ORFs into gene models. It’s good enough to train a predictor like SNAP or Augustus, but should not be used as the final models. If you review the documentation you will see that they should be turned off once you train a predictor.<div class=""><br class=""></div><div class="">Here is an example —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 8, 2019, at 1:48 PM, Das, Debojyoti <<a href="mailto:debojyoti.das@und.edu" class="">debojyoti.das@und.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255); display: inline !important;" class="">Hi<span class="Apple-converted-space"> </span><span style="font-family: Arial, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">Carson</span>,</span><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">I am working on a non-model reptile species. I tried running maker with est2genome=1 and protein2genome=1 with the following evidence:</div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">1. est=transcriptome.fasta (de novo assembled)</div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">2. protein in fasta format from two related species. </div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""> <br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""> I keep getting predictions where gene models identify multi-exon genes but fail to incorporate all the exons even though they are present on the scaffolds. The fact that in the predicted gene models some exons were correctly identified while missing others even though the entire gene is present on the scaffolds, we checked this by loading the annotation in IGV Viewer. </div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">Since we are not completely confident of our transciptome assembly, we thought of using cDNA from a closely related species.</div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">1. altest="cDNA in fasta format from a related species"<br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">2. protein in fasta format from two related species.</div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">However, when I do this I get the error </div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><b class="">"ERROR: You must provide some form of EST evidence to use est2genome as a predictor."</b></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><b class=""><br class=""></b></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">Interestingly, if I switch est2genome off (setting it to zero) maker starts running. </div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">Any suggestions on how to proceed.</div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">Best,</div><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; background-color: rgb(255, 255, 255);" class="">Debojyoti</div></div><div id="Signature" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; 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