<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>You can provide a comma separated list of files to est_gff. Also from experience cufflinks gives far better results than tophat. Tophat tends to have a lot of false positives that adversely affect the overall quality of gene models, so I usually recommend that people use cufflinks output and not even include the tophat results in their run.</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> Michael Seidl <<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><br><span style="font-weight:bold">Date: </span> Tuesday, April 22, 2014 at 2:30 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br></div><div><br></div><div dir="ltr">Dear Carson,<div><br></div><div>thanks a lot I will try. More importantly, you pointed me to a mistake in my procedure which will make me rerun the maker anyway :p</div><div><br></div><div>I want maker to use the tophat.gff next to cufflinks est (fa + gff) as well as a protein.fa. I provide them currently as follows: </div><div><br></div><div><p style="margin:0px;font-size:11px;font-family:Menlo">#-----EST Evidence (for best results provide a file for at least one)</p><p style="margin:0px;font-size:11px;font-family:Menlo">est= /home/michael/data/side/alternaria/maker_annotation/Alternaria-CBS-916.96/transcripts.cds.fa #set of ESTs or assembled mRNA-seq</p><p style="margin:0px;font-size:11px;font-family:Menlo">altest= #EST/cDNA sequence file in fasta format from an alternate organism</p><p style="margin:0px;font-size:11px;font-family:Menlo">est_gff= /home/michael/data/side/alternaria/maker_annotation/Alternaria-CBS-916.96/transcripts.gff3 #aligned ESTs or mRNA-seq from a</p><p style="margin:0px;font-size:11px;font-family:Menlo">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</p><p style="margin:0px;font-size:11px;font-family:Menlo;min-height:13px"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">#-----Protein Homology Evidence (for best results provide a file for at least one)</p><p style="margin:0px;font-size:11px;font-family:Menlo">protein= /home/michael/data/side/alternaria/maker_annotation/fungal_proteins.fa #protein sequence file in fasta format (i.e. from mu</p><p style="margin:0px;font-size:11px;font-family:Menlo">protein_gff= #aligned protein homology evidence from an external GFF3 file</p></div><div><br></div><div>Can I give the tophat.gff as a alttest.gff or is maker internally using est_gff and altest_gff differently? Sorry for this question, but I did not yet realized that the other_gff will be omitted during maker</div><div><br></div><div>Thanks a lot </div><div>Michael</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 22, 2014 at 9:10 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">The issue was indeed caused by a bug in using the other_gff= file option. Could you place the attached file in .../maker/lib/. Then you can rerun maker to test if it fixes it ('maker -a' for fast rerun without analysis rerun).<br><br>
Alternately if you don't feel like rerunning everything, you can also filter out the lines using --> grep -v "ARRAY" file.gff<br><br>
Since the other_gff file is not used in any part of the analysis and is just a convenience option that prints any text given to it into the final GFF3 file, then filtering them out is the same as if you would have left other_gff blank when running MAKER. You can then use 'gff3_merge -s tophat.gff merged_genome.gff' to merge the desired extra lines back into your file outside of MAKER.<br><div class=""><br>
Thanks,<br>
Carson<br><br><br><br>
From: Michael Seidl <<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>>><br></div>Date: Tuesday, April 22, 2014 at 12:29 PM<br><div class="">To: Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>><br>
Subject: Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br><br></div><div class="">Hi Carson,<br><br>
I uploaded the files as an archive.<br><br>
Thanks<br>
Michael<br><br><br></div><div class="">On Tue, Apr 22, 2014 at 5:04 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>> wrote:<br>
In the base maker.output directory for the job, there will be a file with a .db extension. Could you send that as well? I'm leaning towards this being something odd happening with the GFF3 files used as input. Particularly the other_gff= file. Could you upload this file as well --> /home/michael/data/side/alternaria/maker_annotation/Alternaria-CBS-916.96/tophat.gff3.<br><br>
--Carson<br><br><br></div><div class="">From: Michael Seidl <<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>>>><br></div><div class="">Date: Tuesday, April 22, 2014 at 8:56 AM<br></div>To: Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>>><br><div class="">Subject: Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br><br>
Should be uploading right now...<br><br>
Thanks Michael<br><br><br><br></div><div class="">On Tue, Apr 22, 2014 at 4:46 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>>> wrote:<br>
Could you pack up this directory for me --> /84/ED/scaffold3.1/ and upload it here --> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi" target="_blank">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a><br><br>
Thanks,<br>
Carson<br><br><br></div>From: Michael Seidl <<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>>><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>>>>><br><div class="">Date: Tuesday, April 22, 2014 at 8:43 AM<br></div>To: Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>>>><br>
Cc: "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<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><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>>>><br><div class="">Subject: Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br><br><br></div><div><div class="h5">On Tue, Apr 22, 2014 at 4:39 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>>>> wrote:<br>
any<br><br>
Dear Carson,<br><br>
maker -version returns 2.31. Yes, also the individual scaffolds seem to contain ARRAY refs, e.g.<br>
find -name "*gff" | xargs grep "ARRAY":<br><br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x41f6ea0)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xb87d888)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xd343528)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xb12fc48)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xde02488)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x8d4c698)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x447a8a0)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x4390048)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xdbb4e00)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xe3f1790)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x438d570)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xae00088<br><br>
Cheers<br>
M<br><br><br><br><br><br>
--<br>
Michael F Seidl, PhD<br>
Research Fellow (Postdoc)<br>
Laboratory of Phytopathology<br>
Wageningen University<br>
P.O. Box 8025, 6700 EE Wageningen<br>
Wageningen Campus, building 107 (Radix)<br>
Droevendaalsesteeg 1, 6708 PB Wageningen<br><br>
Tel.: +31-317-481288<br>
Fax: +31-317-483412<br><br></div></div>Email: <a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>>><br><div class="">Website: <a href="http://www.php.wur.nl/UK/" target="_blank">http://www.php.wur.nl/UK/</a><br>
Twitter: @MFSeidl<br><br></div><a href="http://www.disclaimer-uk.wur.nl" target="_blank">www.disclaimer-uk.wur.nl</a><<a href="http://www.disclaimer-uk.wur.nl" target="_blank">http://www.disclaimer-uk.wur.nl</a>><<a href="http://www.disclaimer-uk.wur.nl/" target="_blank">http://www.disclaimer-uk.wur.nl/</a>><br><div class="HOEnZb"><div class="h5"><br><br><br><br>
--<br>
Michael F Seidl, PhD<br>
Research Fellow (Postdoc)<br>
Laboratory of Phytopathology<br>
Wageningen University<br>
P.O. Box 8025, 6700 EE Wageningen<br>
Wageningen Campus, building 107 (Radix)<br>
Droevendaalsesteeg 1, 6708 PB Wageningen<br><br>
Tel.: <a href="tel:%2B31-317-481288" value="+31317481288">+31-317-481288</a><br>
Fax: <a href="tel:%2B31-317-483412" value="+31317483412">+31-317-483412</a><br><br>
Email: <a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><br>
Website: <a href="http://www.php.wur.nl/UK/" target="_blank">http://www.php.wur.nl/UK/</a><br>
Twitter: @MFSeidl<br><br><a href="http://www.disclaimer-uk.wur.nl" target="_blank">www.disclaimer-uk.wur.nl</a><<a href="http://www.disclaimer-uk.wur.nl/" target="_blank">http://www.disclaimer-uk.wur.nl/</a>><br></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b style="font-size:8px"><font color="#808080"><font face="verdana,sans-serif"><span style="font-size:10px">Michael F Seidl, PhD</span></font></font></b><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999" face="verdana,sans-serif"><span style="font-size:10px;background-color:rgb(255,255,255)">Research Fellow (Postdoc)</span></font></span></span></div><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999" face="verdana,sans-serif"><span style="font-size:10px;background-color:rgb(255,255,255)">Laboratory of Phytopathology</span></font></span></span></div><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999" face="verdana,sans-serif"><span style="font-size:10px;background-color:rgb(255,255,255)">Wageningen University</span></font></span></span></div><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999"><span style="font-size:10px;background-color:rgb(255,255,255)"><font face="verdana,sans-serif"></font></span></font></span></span></div><div><font color="#999999" size="1" face="verdana,sans-serif">P.O. Box 8025, 6700 EE Wageningen<br>Wageningen Campus, building 107 (Radix)<br>Droevendaalsesteeg 1, 6708 PB Wageningen</font></div><div><font face="verdana,sans-serif"><font color="#999999" size="1"></font> </font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Tel.: +31-317-481288</font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Fax: +31-317-483412</font></div><div><font face="verdana,sans-serif"><font color="#999999" size="1"></font> </font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Email: <a href="mailto:michael.seidl@wur.nl" target="_blank">michael.seidl@wur.nl</a></font></div><div><font color="#999999" size="1"><font face="verdana,sans-serif">Website: </font><a href="http://www.php.wur.nl/UK/" target="_blank"><font face="verdana,sans-serif">http://www.php.wur.nl/UK/</font></a></font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Twitter: @MFSeidl</font></div><div><font face="verdana,sans-serif"> </font></div><div><a href="http://www.disclaimer-uk.wur.nl/" target="_blank"><font color="#999999" size="1" face="verdana,sans-serif">www.disclaimer-uk.wur.nl</font></a></div></div></div></span></body></html>