<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>gff3_merge just merges any two GFF3 files. So if you have two files just give both of them to it.</div><div><br></div><div>Example --></div><div>gff3_merge maker_genes.gff repeats.gff</div><div><br></div><div>Also if all you are trying to do is filter out certain feature types from the file, just use grep instead.</div><div><br></div><div>Example --></div><div>grep -v -P "\tpred_gff\t" maker.gff</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu">fbarreto@ucsd.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, June 5, 2014 at 1:01 PM<br><span style="font-weight:bold">To: </span> MAKER group <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Generating GFF with selected tracks<br></div><div><br></div><div dir="ltr">Hi, all,<div><br></div><div>I would like to produce a gff file that contains Maker gene models AND repeats. I know that using gff3_merge with -g will generate one with only the gene models, but I didn't see any options for adding additional tracks.</div><div><br></div><div>The way I did this was to use the Re-annotation section in the control file. I provided the original full gff file in maker_gff, and turned on the rm_pass and model_pass. All other options in the control file were turned off. This seemed to work, though it also added a 'model_gff:maker' track, which is not a problem for me. I compared a few new and original scaffolds in Apollo, and all seem to match perfectly. But since I cannot check the whole genome, I was wondering if what I did was appropriate. Are all the gene models (and their names) and repeat alignments identical between the new and original files? Or is Maker potentially changing a few things since it's treated as a new run?</div><div><br></div><div>Thanks!<br clear="all"><div><br></div>-- <br>Felipe Barreto<br><br></div></div>
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