<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="">gff3_merge is expecting to work with maker output, and the -g option specifically looks for maker produced genes (maker source tag). Since you added these lines using the other_gff option, they are in the file, but it doesn’t necessarily mean downstream maker tools will know what to do with them because maker added them blindly without attempting any interpretation/validation, etc. I purposely don’t try and make these tools support any GFF3 input possible, it just gets too hairy.<div class=""><br class=""></div><div class="">What you can do though is grep the features you want out separately into another GFF3 file and then you can use gff3_merge to combine those two files.<br class=""><div class=""><br class=""></div><div class=""><font face="Courier" class="">grep -P “\tbarrnap:0.5\t” infile.gff > barnap.gff</font></div><div class=""><font face="Courier" class="">gff3_merge -s maker.gff barnap.gff > new.gff</font></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 1, 2015, at 1:34 PM, Shaun Jackman <<a href="mailto:sjackman@gmail.com" class="">sjackman@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="markdown-here-wrapper" style=""><p style="margin:1.2em 0px!important" class="">Hi, Carson.</p><p style="margin:1.2em 0px!important" class="">I’m using <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248)" class="">other_gff</code> to pass the following four-record GFF file of rRNA annotations through to the final GFF file. The rRNA records appear in the output of <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248)" class="">gff3_merge -s -n</code>, but not when I add the <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248)" class="">-g</code> option. Any thoughts why they’ve gone missing? These rRNA features almost certainly overlap repeat rRNA features discovered by RepeatMasker. Would that cause it? I’m happy to send along whatever data files you’d find useful to reproduce the issue.</p><p style="margin:1.2em 0px!important" class="">Cheers,<br class="">Shaun </p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px" class=""><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248);white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important;display:block;padding:0.5em;color:rgb(51,51,51);background:rgb(248,248,255)" class="">##gff-version 3
17 barrnap:0.5 rRNA 130358 131272 . - . Name=16S_rRNA;product=16S ribosomal RNA (partial);note=aligned only 57 percent of the 16S ribosomal RNA
18 barrnap:0.5 rRNA 6238 7489 . - . Name=12S_rRNA;product=12S ribosomal RNA
5 barrnap:0.5 rRNA 7 1246 . - . Name=12S_rRNA;product=12S ribosomal RNA
6 barrnap:0.5 rRNA 449193 450443 . + . Name=12S_rRNA;product=12S ribosomal RNA
</code></pre><div title="MDH:SGksIENhcnNvbi48ZGl2Pjxicj48L2Rpdj48ZGl2PkknbSB1c2luZyBgb3RoZXJfZ2ZmYCB0byBw
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