<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="">A quick overview of MAKER behavior. MAKER will keep everything in model_gff as long as you don’t provide another predictor to run or pred_gff file to use. But if you give it a predictor to run, it takes that as an indicator that you want to update models. So model_gff may get replaced by another prediction that overlaps it but scores better.<div class=""><br class=""></div><div class="">So depending on the behavior you want, make sure you are using model_gff and do or don’t provide a gene predictor to run.</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 22, 2018, at 2:04 PM, Poelchau, Monica <<a href="mailto:monica.poelchau@ars.usda.gov" class="">monica.poelchau@ars.usda.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-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;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Kapeel,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">If you just want your community annotations to replace models in an existing gene set, we have a tool for this:<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="https://github.com/NAL-i5K/GFF3toolkit" style="color: purple; text-decoration: underline;" class="">https://github.com/NAL-i5K/GFF3toolkit</a><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">You’d need to run gff3_QC on your annotation files first to make sure your annotations are okay, then use gff3_merge to merge your community annotations with your existing gene set (in gff3 format). If you end up trying this out - we’re actively developing the GFF3toolkit, so feel free to post an issue if you notice any problems.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hth,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Monica<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel-bounces@yandell-lab.org</a>> on behalf of Kapeel Chougule <<a href="mailto:kapeelc@gmail.com" style="color: purple; text-decoration: underline;" class="">kapeelc@gmail.com</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Friday, June 22, 2018 at 13:53<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:maker-devel@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>[CAUTION: Suspicious Link][maker-devel] map_forward=1 not mapping reference ID's to output correctly<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><p style="margin-left: 0.5in;" class=""><b class="">PROCEED WITH CAUTION:</b><span class="Apple-converted-space"> </span>This message triggered warnings of<span class="Apple-converted-space"> </span><b class="">potentially</b><span class="Apple-converted-space"> </span>malicious web content. Evaluate this email by considering whether you are expecting the message, along with inspection for suspicious links.<o:p class=""></o:p></p><p style="margin-left: 0.5in;" class="">Questions:<span class="Apple-converted-space"> </span><a href="mailto:Spam.Abuse@wdc.usda.gov" style="color: purple; text-decoration: underline;" class="">Spam.Abuse@wdc.usda.gov</a><o:p class=""></o:p></p><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br clear="all" class=""><o:p class=""></o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10.5pt; font-family: Arial, sans-serif; color: rgb(43, 44, 51); letter-spacing: -0.15pt; background-color: rgb(241, 241, 244); background-position: initial initial; background-repeat: initial initial;" class="">I am trying to update<span class="Apple-converted-space"> </span><a href="https://de.cyverse.org/dl/d/39D60E88-078D-4CF5-9F3A-D712B714CDD8/community.annotation.gff3" style="color: purple; text-decoration: underline;" class="">community annotation</a><span class="Apple-converted-space"> </span>in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10.5pt; font-family: Arial, sans-serif; color: rgb(43, 44, 51); letter-spacing: -0.15pt; background-color: rgb(241, 241, 244); background-position: initial initial; background-repeat: initial initial;" class=""><br class=""><br class=""></span><o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 16.5pt;" class=""><span style="font-size: 10.5pt; font-family: "Courier New"; color: rgb(43, 44, 51); letter-spacing: -0.15pt; background-color: rgb(241, 241, 244); background-position: initial initial; background-repeat: initial initial;" class="">Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR 34129 gene 47121 mRNA 53708 three_prime_UTR<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 16.5pt; background-color: rgb(241, 241, 244);" class=""><span style="font-size: 10.5pt; font-family: "Courier New"; color: rgb(43, 44, 51); letter-spacing: -0.15pt;" class="">MAKER gene count-> <o:p class=""></o:p></span></div></div></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 16.5pt; background-color: rgb(241, 241, 244);" class=""><span style="font-size: 10.5pt; font-family: "Courier New"; color: rgb(43, 44, 51); letter-spacing: -0.15pt;" class="">awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105<o:p class=""></o:p></span></div></div></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 16.5pt; background-color: rgb(241, 241, 244);" class=""><span style="font-size: 10.5pt; font-family: "Courier New"; color: rgb(43, 44, 51); letter-spacing: -0.15pt;" class=""><o:p class=""> </o:p></span></div></div></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:<br class=""><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data" style="color: purple; text-decoration: underline;" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data</a><br class="">. So not sure why we dont have the all the community gene models mapped in the MAKER output<br class=""><br class="">Thanks<br class=""><br class="">Kapeel<br class="">--<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div class=""><div class=""><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-family: "Courier New";" class=""><o:p class=""> </o:p></span></b></div></div><div class=""><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-family: "Courier New";" class="">Kapeel Chougule<o:p class=""></o:p></span></b></div></div><p class="MsoNormal" style="margin: 0in 0in 12pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;"><b class=""><span style="font-family: "Courier New";" class="">Computational Scientist Developer II<br class="">One Bungtown Road Cold Spring Harbor, NY 11724<br class=""><a href="http://www.warelab.org/" target="_blank" style="color: purple; text-decoration: underline;" class="">http://www.warelab.org/</a></span></b><o:p class=""></o:p></p></div></div></div></div></div></div><br style="caret-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;" class=""><br style="caret-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;" class=""><br style="caret-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;" class=""><br style="caret-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;" class=""><span style="caret-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; float: none; display: inline !important;" class="">This electronic message contains information generated by the USDA solely for the intended recipients. 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