<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>There are many ways of doing this. You can run everything separately and then copy all GFF3 files into a common folder and use the gff3_merge script that comes with maker to combine them. Alternatively you can run maker with the -g and -base options. This allows you to specify a new genome on the command line and the base name of the directory to write to. Using those flags you can swap in a different contig file while maintaining the same output directory for your job as a whole. Just run maker at the end of the run using the original fasta and the -dsindex flag, to sync the datastore index file so it is complete if you do this option.</div><div><br></div><div>To split out contigs of interest you can also use the fasta_tool that comes with maker and use the -grep_header or –select flags to indicate which contigs to retrieve.</div><div><br></div><div>--Carson</div><div><br></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> Bérénice Benayoun <<a href="mailto:benayoun@stanford.edu">benayoun@stanford.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 21 November, 2012 1:45 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Cc: </span> Dario Riccardo Valenzano <<a href="mailto:dario1@stanford.edu">dario1@stanford.edu</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Prioritizing specific scaffolds to be annotated?<br></div><div><br></div>Hello,<div><br></div><div>I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). </div><div><br></div><div>We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ?</div><div><br></div><div>I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. </div><div><br></div><div>Do you have any advice for this ?</div><div><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"><font color="#222222" face="arial,sans-serif">Thank you so much in advance for your most invaluable help !</font></div><div><font color="#222222" face="arial,sans-serif"><br></font></div><div><font color="#222222" face="arial,sans-serif">Sincerely yours,</font></div><div><font color="#222222" face="arial,sans-serif"><br></font></div><div>
Bérénice</div><div><font color="#222222" face="arial,sans-serif"><br></font>-- <br><font>Bérénice A. BENAYOUN, Ph.D.</font><br>
Stanford University/Genetics Department<br><i>BRUNET Laboratory</i>, 'Molecular Basis of Longevity and Age Related Diseases'<br>
M312 Alway Building<br>
300, Pasteur Drive<br><span>MC 5120 <br>
Stanford, CA 94305-5120</span><br>USA<br>
Email: <a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a><br>
Web: <a href="http://www.stanford.edu/group/brunet/" target="_blank">www.stanford.edu/group/brunet/</a><a href="http://www.stanford.edu/group/brunet/" target="_blank"></a><br></div>
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