<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="">keep_preds=1 will take all the raw predictions remove any that overlap the current supported gene set, then filter for redundancy (i.e. if you ran both SNAP and Augustus), then add what’s left to the final gene models. It’s basically the equivalent of taking all the models in the non-overlapping.abiinit file in a normal MAKER run and adding them to the final models.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 1, 2017, at 1:27 PM, 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="">Hi,</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="">From what I understand, an AED of 1 means that the gene predicted by gene finder is not supported by external evidence (transcriptome and protein).</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="">So how is it different with keep_preds=1, which is describe as "add unsupported gene prediction" ?</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="">Because I have way more gene with keep_pred=1.<span class="Apple-converted-space"> </span><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=""><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="">Maybe I missed something.</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="">Thanks.</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 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="">Patrick<span class="Apple-converted-space"> </span></div></div></div></blockquote></div><br class=""></div></body></html>