<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="">To access files for individual sequences use the datastore index:<div class="">/scratchsan/caceronn/Results/MAKER/data/hsap_contig.maker.output/hsap_contig_master_datastore_index.log</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">look in that file to find the location of individual contig results. For merged results you have to use the gff3_merge script together with the datastore index.</div><div class=""><br class=""></div><div class="">Here is a nice tutorial with step by step instructions and a video to easilly follow along —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 16, 2016, at 2:17 PM, Alejandro Cerón Noriega <<a href="mailto:alejocn5@gmail.com" class="">alejocn5@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span id="result_box" class="" lang="en"><span class="">hello i am Alejandro<br class=""></span></span><div class=""><div class=""><span id="result_box" class="" lang="en"><span class=""><br class="">I have tried to</span> <span class="">follow the</span> <span class="">tutorial</span> <span class="">MAKER</span></span><br class=""><br class="">1-I Copy the files in the data directories to a temporary directory where i run an example file.<br class="">2-I Type maker -CTL to generate generic MAKER control files (foto_1)<br class="">3-I edit the control files to include the path of the genome file ( hsap_contig.fasta from the example) (foto_2)<br class=""></div><div class="">then I give the paht maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl (foto 3)<br class=""><br class=""></div><div class="">that generate a expected folder <br class="">hsap_contig.maker.output<br class=""><br class=""></div><div class="">but when i whatn to look for the gff file i dont find it, inside the /data/hsap_contig.maker.output/hsap_contig_datastore, i dont find the all subdirectories<br class=""><br class="">seq_name.gff - a gff file that can be loaded into GMOD, GBROWSE,<br class=""> or Apollo<br class=""> * seq_name.maker.transcripts.fasta - a fasta file of the MAKER<br class=""> annotated transcript sequences<br class=""> * seq_name.maker.proteins.fasta - a fasta file of the MAKER<br class=""> annotated protein sequences<br class=""> * seq_name.maker.XXX.transcript.fasta - a fasta file of ab-initio<br class=""> predicted transcript sequences from program XXX<br class=""> * seq_name.maker.XXX.proteins.fasta - a fasta file of ab-inito<br class=""> predicted protein sequences from program XXX<br class=""> * seq_name.maker.non_overlapping_ab_initio.transcripts.fasta - a<br class=""> fasta file of filtered ab-inito transcript sequences that don't<br class=""> overlap maker annotations<br class=""> * seq_name.maker.non_overlapping_ab_initio.proteins.fasta - a<br class=""> fasta file of filtered ab-inito protein sequences that don't<br class=""> overlap maker annotations<br class=""> * theVoid.seq_name/ - a directory containing all of the raw<br class=""> output files produced by MAKER, including BLAST reports, SNAP<br class=""> output, exonnerate output and the masked genomeic sequence.<br class=""><br class=""></div><div class="">i only find a directorie named 80 (foto 4)<br class=""><br class=""></div><div class="">i dont know if a make somthing wrong, <br class=""></div><div class=""><br class=""></div><div class=""><span id="result_box" class="" lang="en"><span class="">also</span> <span class="">try</span> <span class="">to change the</span> <span class="">path</span> <span class="">of the EST (foto_5)<br class=""><br class=""></span></span></div><div class=""><br class=""><div style="" id="gt-input-tool" class=""><div class=""><span class=""></span></div></div><div id="gt-src-c" class=""><div id="gt-src-p" class=""> </div> </div> <div id="gt-res-content" class=""><div dir="ltr" style="zoom:1" class=""><span id="result_box" class="" lang="en"><span class="">thanks for your attention</span></span></div></div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><font face="arial, helvetica, sans-serif" class=""><b class="">Alejandro Cerón Noriega, </b></font><i style="font-family: sans-serif; line-height: 19.1875px;" class="">B.Sc</i> <br class="">MSc. Candidate Bioinformatics<div class=""><b class="">K ♣</b><b class=""><font color="#cc0000" class="">♣</font></b><b class=""><font color="#ffcc00" class="">♣</font></b><font face="arial, helvetica, sans-serif" class=""><b class=""><br class=""></b></font><div class=""><font face="arial, helvetica, sans-serif" class=""><b class=""><br class=""></b></font></div></div></div></div></div></div>
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