<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="">Hello!<div class=""><br class=""></div><div class="">I’m using Maker to map forward annotations to a new genome assembly in a species of choanoflagellate. I followed the protocol from Campbell 2014, creating a transcript FASTA file from my old GFF3 file and using this as the only EST evidence. I set est2genome=1 and est_forward=1. The Maker ran great, except it seems that many of the old transcripts are mapping many places in the new assembly, up to 100+ times, so that my gene count has inflated from 11,624 to 25,905. Of the most highly multiply mapped genes, many but not all are rRNA genes.</div><div class=""><br class=""></div><div class="">I was wondering if there is a setting or tweak I can make so that each transcript maps uniquely to its best location in the new genome? Or maybe tweaking the exonerate stringency? This is not the final annotation step, as I will also be using RNA-seq evidence to improve my gene models after liftover.</div><div class=""><br class=""></div><div class="">Thanks for your help!</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Max</div><div class=""><br class=""></div><div class=""><div class="">
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="caret-color: rgb(0, 0, 0); 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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Max Coyle</div><div style="caret-color: rgb(0, 0, 0); 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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">PhD Candidate, King Lab</div><div style="caret-color: rgb(0, 0, 0); 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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Dept of Molecular and Cellular Biology, UC Berkeley</div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline">
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