<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="">Hi Emmanuel, Please “reply all” to in these exchanges so that they’ll stay stored on the maker-devel list for others to find in the future. It also helps keep the conversation open so that others can chime in and help out too. :) <div class=""><br class=""></div><div class="">I looked at several of the “nonfunctional due to frameshift” genes and they have associated features in the gff3 file. So there might be a frameshift issue in the original annotations, but I’d doubt that, or a frameshift error might be getting introduced when you convert to the tbl format. <br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 2, 2017, at 5:12 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Daniel<div class=""><br class=""></div><div class="">I NCBI first complained of this even when I hadn't used GAG annotation to remove N's,</div><div class=""><br class=""></div><div class="">On my raw file they complained about this</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Thu, Nov 2, 2017 at 10:07 PM, Daniel Ence <span dir="ltr" class=""><<a href="mailto:dandence@gmail.com" target="_blank" class="">dandence@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Emmanuel, I recommend looking into what Carson suggested. If you edited the fasta files for the “NNN” characters for the transcripts or reference genome and then resubmitted without changing the gff3 coordinates, then that would result in these kind of errors. <div class=""><br class=""></div><div class="">~Daniel</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Nov 2, 2017, at 5:02 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-303446518622250827Apple-interchange-newline"><div class=""><a href="https://drive.google.com/file/d/1rPSI3HhceRuJMzWO9hAej-BzMNUSKz7g/view?usp=drive_web" style="font-family:arial;font-size:13px;font-style:normal;font-variant:normal;font-weight:bold;letter-spacing:normal;line-height:13px;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;background-color:rgb(245,245,245);display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none" target="_blank" class=""><img src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" style="vertical-align:bottom;border:none" class=""> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom" class="">muc_functional.blast.gff</span></a></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div>
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