<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div><p style="margin: 0px; line-height: normal;" data-mce-style="margin: 0px; line-height: normal;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222; background: white;">Hi ! </span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;">I have tried three rounds of annotation in Maker on a non model arthropod genome (1.7Gb) which is an hybrid assembly of Pacbio and illumina reads.</span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;">As suggested in the tutorial, I ran in the first round Maker with repeat masking to generate gene models using transcript (Trinity assembly) and protein (swissprot) evidence. Then Maker models were used twice in a bootstrap fashion to retrain SNAP. </span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;">The number of genes drops from </span><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;">29207 in the round 1 to 22547 in the round 2 then increases slightly to 22931 in the round 3.</span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><br> <span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;"><span style="font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; white-space: pre-wrap; widows: 2; -webkit-text-stroke-width: 0px; float: none; word-spacing: 0px;" data-mce-style="font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; white-space: pre-wrap; widows: 2; -webkit-text-stroke-width: 0px; float: none; word-spacing: 0px;">However, the AED profile (attached) don't seem to be satisfactory.</span></span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;">So I wonder if you could let me a good strategy to improve the annotation quality. Do you think that filtering good transcripts could improve results. If yes , which criteria should</span><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;"> be taken into account ?</span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;">Thank you.</span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;"><br data-mce-bogus="1"></span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;">Best;</span></p><p style="line-height: normal; background: white; margin: 0px;" data-mce-style="line-height: normal; background: white; margin: 0px;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;">Amine</span></p></div></div></body></html>