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<p class="MsoNormal">Hi, I sent an email earlier about this but didn’t really hear back.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I dug into the problem more (basically my transcriptome and other tracks were not showing up on my test organism). After looking at the error_log and doing some debugging, I confirmed that new tracks I load onto a test organism have a
srcfeature_id which points to the same scaffold, but on my production organism.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am definitely typing in the name of the test organism when I do the load (I am using chado, gmod_gff3_bulk_load).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I confirmed that if I change the srcfeature_id in the database, I can now see the track.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So I am wondering if anyone has seen this before? And what do you recommend I do next? I could:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Rebuild my entire system<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Try to debug what is happening (maybe in the load script?)<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">3)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Just write a script that fixes the problem by updating the src_featureids<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Shane<o:p></o:p></p>
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