<div dir="ltr">Hi Carson<div>Thanks for the reply</div><div><br></div><div>I generated the off with this command <span style="color:rgb(0,0,0);font-family:'Times New Roman',stixgeneral,serif;font-size:15.999099731445313px">gff3_merge –d </span><span style="color:rgb(0,0,0);font-family:'Times New Roman',stixgeneral,serif;font-size:15.999099731445313px">dpp_contig.maker.output/dpp_contig_master_datastore_index.log</span></div><div><span style="color:rgb(0,0,0);font-family:'Times New Roman',stixgeneral,serif;font-size:15.999099731445313px"><br></span></div><div><font color="#000000" face="Times New Roman, stixgeneral, serif"><span style="font-size:15.999099731445313px">I had to rerun browse with the following command</span></font></div><div><font color="#000000" face="Times New Roman, stixgeneral, serif"><span style="font-size:15.999099731445313px"><br></span></font></div><div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb</span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Although its showing</span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"></span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">WARNING: No matching features found for mRNA I don't know what it means</span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">I don't understand what it means</span></p></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div>Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host</div><div><br></div><div><br></div><div>The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Nnadi Nnaemeka Emmanuel<div>Department of Microbiology,</div><div>Faculty of Natural and Applied Science,</div><div>Plateau State University, Bokkos, Plateau State, Nigeria.</div><div>Publications:  <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
<br><div class="gmail_quote">On Tue, Oct 10, 2017 at 1:35 AM, 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"><div style="word-wrap:break-word">Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it’s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.<div><br></div><div>Thanks,</div><div>Carson</div><div><div class="h5"><div><br><div><br></div><div><br><div><br><div><blockquote type="cite"><div>On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:</div><br class="m_-8752983405514246806Apple-interchange-newline"><div><div dir="ltr">Please,<div>I ran the command line</div><div><br></div><div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">maker2jbrowse muc1_genome_snap2.all.gff</span></div></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div>The command created some folders. However, at the end it read</div><div><span style="font-family:Menlo;font-size:11px">No reference sequences defined in configuration, nothing to do.</span><br></div><div><span style="font-family:Menlo;font-size:11px"><br></span></div><div><span style="font-family:Menlo;font-size:11px">Please what does it mean? How can I view it in jbrowse. </span></div><div><span style="font-family:Menlo;font-size:11px"><br></span></div><div><span style="font-family:Menlo;font-size:11px">Thanks</span></div><div><span style="font-family:Menlo;font-size:11px"><br></span></div><div><span style="font-family:Menlo;font-size:11px"><br></span></div><div><div><div class="m_-8752983405514246806gmail_signature"><div dir="ltr">Nnadi Nnaemeka Emmanuel<div>Department of Microbiology,</div><div>Faculty of Natural and Applied Science,</div><div>Plateau State University, Bokkos, Plateau State, Nigeria.</div><div>Publications:  <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/<wbr>profile/Emmanuel_Nnadi/<wbr>publications</a></div></div></div></div>
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