<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="">Your plan sounds good. A couple of related notes.<div class=""><br class=""></div><div class="">Insect genomes tend to have high gene density, so gene merging will be the primary difficulty. You can avoid merging of mRNA-seq evidence by using options like jaccard_clip in Trinity. Then use avoid_est_fusion=1 inside of MAKER.</div><div class=""><br class=""></div><div class="">Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can’t be run in the same directory).</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 Jun 2, 2017, at 3:56 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255);" class="">Hello,<br class=""><br class="">This is my first time running Maker for an insect genome annotation.<span class="Apple-converted-space"> </span><br class=""><br class="">I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:<br class=""><br class=""><br class="">What I have:<br class="">- RNA evidence: transcriptome<br class="">- Proteine evidence: swissprot/uniprot + busco protein set of insect<br class="">- Cegma and busco results of my genome<br class=""><br class=""><br class="">1) Train SNAP with CEGMA<br class=""><br class="">2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).<br class=""><br class="">3) Create SNAP model from run A.<br class=""><br class="">4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).<br class=""><br class="">5) Create SNAP model from run B.<br class=""><br class="">6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).<br class=""><br class="">7) Create SNAP model from run C AND Create Augustus gene model from run C<br class=""><br class="">8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1). + Use keep_preds=1<br class=""><br class=""><br class=""><br class="">Does it seems coherent ?</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255);" class="">Cheers,<br class=""></div><div id="Signature" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255);" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class=""><br class="">Patrick Tran Van<br class=""><br class="">Groups Chapuisat, Robinson-Rechavi & Schwander<br class="">Department of Ecology and Evolution<br class="">University of Lausanne<br class="">Le Biophore<br class="">CH-1015 Lausanne<br class="">Switzerland<br class="">Office 3206<br class=""><br class=""></div></div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; 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