<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=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 1, 2015, at 2:53 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">There is probably something weird about the way you are running it. For example did you give it the raw RNA-seq reads instead of the assembled reads?<div class=""><br class=""></div><div class="">The total size of the final GFF3 will be all genes + all evidence alignments + the assembly fasta (concatenated at the end per GFF3 format specifications). You can remove the fasta or the evidence alignments from the file using the options found in gff3_merge. </div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><div class=""><blockquote type="cite" class=""><div class=""><br class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">John Cornelius <<a href="mailto:jcornel3@asu.edu" class="">jcornel3@asu.edu</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Why would MAKER generate a large gff3?</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">May 1, 2015 at 2:46:45 PM MDT<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""></span></div><br class=""><br class=""><div dir="ltr" class="">Hello, I'm using MAKER to generate a new annotation for an organism without an officially published genome (but it does exist and I'm using it). The current annotation is primarily predictive and I'm adding RNA-Seq evidence to improve it. However, after the initial run and the following two runs with SNAP, the gff3 file generated is 24 GB in size while the old annotation file is only 82 Mb. Should is be that large? Also, what is the best way to analyze a new annotation to figure out if it is actually in decent shape? Thanks. <br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class="">John Cornelius<br class="">MCB PhD Candidate<br class="">Arizona State University<br class=""></div></div>
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<br class=""><br class=""><br class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel-request@yandell-lab.org" class="">maker-devel-request@yandell-lab.org</a><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">confirm d8a6466a8a63fe2312cc2ce7f79739414020644e</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">May 1, 2015 at 2:47:11 PM MDT<br class=""></span></div><br class=""><br class="">If you reply to this message, keeping the Subject: header intact,<br class="">Mailman will discard the held message. Do this if the message is<br class="">spam. If you reply to this message and include an Approved: header<br class="">with the list password in it, the message will be approved for posting<br class="">to the list. The Approved: header can also appear in the first line<br class="">of the body of the reply.<br class=""><br class=""></div></blockquote></div><br class=""></div></div></div></div></blockquote></div><br class=""></body></html>