<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Make sure it's not GTF or GFF2, but if it is GFF3 You can substitute match for mRNA and match_part for CDS. Then it will be interpreted as a two level alignments feature which can be given to pred_gff.</div><div><br></div><div>--Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br><span style="font-weight:bold">Reply-To: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, April 10, 2014 at 12:34 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Using GlimmerHMM with MAKER<br></div><div><br></div><div dir="ltr">The GlimmerHMM gene prediction software outputs a GFF file that includes mRNA and CDS features, but it does not include gene or exon features, and so it does not appear to be working with MAKER. Has anyone else used GlimmerHMM with MAKER, and how did you deal with this issue?<div><br></div><div>Cheers,</div><div>Shaun</div></div>
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