<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="">Hello,<div class=""><br class=""></div><div class="">I have recently begun running Maker. I am currently trying to annotate my Caulanthus Genome (~372Mb); a relative to Arabidopsis. I am unsure about the parameters I have chosen for my first run in maker, which include:</div><div class=""><br class=""></div><div class="">genome=CAB_assembly.fasta (1044 contigs)</div><div class="">est=Representative_transcript_loci.fasta (assembled transcripts btw 200-20000bp long)</div><div class="">protein=TAIR10pep.fasta (Arabidopsis proteins)</div><div class="">—</div><div class=""><u class="">Repeat masking</u></div><div class="">model_org=arabidopsis</div><div class="">rmlib=list of Brassicaceae and common plant repeats</div><div class="">repeat_protein=te_proteins.fasta</div><div class=""><u class="">Gene Prediction</u></div><div class="">snaphmm=A.thaliana.hmm</div><div class="">augustus_species=arabidopsis</div><div class="">est2genome=1</div><div class=""><br class=""></div><div class="">I have run a sample file of scaffolds, as well as the entire genome.</div><div class="">In the sample file of scaffolds, I gff3merged the gffs and then ran evaluator. I noticed that my AED are all 1. Is this bad? What should I try next?</div><div class=""><br class=""></div><div class="">I am also unsure on how to train files and if this should be done in my case.</div><div class=""><br class=""></div><div class="">Can anyone advise me on these issues?</div><div class=""><br class=""></div><div class="">-Elyssa</div></body></html>