<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, I think you’ve posted before about issues 1 and 2 from the NCBI. The note for issue 3 from NCBI sounds like there are gene features that don’t have associated transcript, CDS or exon features. I’m not certain how that could be a result from MAKER. It might be something that someone else created (manually or with another tool), and then passed to maker from a GFF file. In the example included in your email, it looks like these offending genes are transposons that have been annotated as genes. If that is the case for the rest of the offending genes, then I would suggest changing the “type” field (column 3) from “gene” to something else, like “transposable_element” perhaps. <div class=""><br class=""></div><div class="">~Daniel</div><div class=""><br class="">
<br class=""><div><blockquote type="cite" class=""><div class="">On Nov 2, 2017, at 3:51 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">I am trying to submit my genome i annotated using maker and they sent back this error,</div><div class="">1. <span style="font-size:12.800000190734863px" class="">Please remove any N nucleotides from the beginning or end of the sequence</span></div><div class=""><span style="font-size:12.800000190734863px" class=""> 2.No feature should begin or end inside a gap. Instead the feature should</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">be made partial at the gap boundary.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[3] Coding regions should not be 5' partial if they begin with the start</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">methionine. If this is an internal methionine int he translation than</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">it is fine if they are partial. Conversely, all coding regions</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">must have a stop codon or be 3' partial.</span></div><div class=""><span style="font-size:12.800000190734863px" class="">You have a large number of gene features that are not associated</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">with other features. Please include on these features in the</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">gene description field some description of what the gene would</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">have encoded.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">A feature table example of this is:</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""><41156 >40652 gene</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> gene_desc transposon</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> locus_tag CR513_45338</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> note nonfunctional due to frameshift</span><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class="">Please how can i use maker to solve this problem?</span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><div class=""><div class="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>
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