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</o:shapelayout></xml><![endif]--></head><body lang=EN-AU link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hello,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>We are trying to add RNA-Seq data into the Maker run. As they have been properly aligned to our draft scaffolds by Cufflinks, we just gave the appropriate gff file to the est_gff option. The gff file is with the following format:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>….<o:p></o:p></p><p class=MsoNormal>scaffold_56 Cufflinks match_part 248833 249471 . + . ID=1:TCONS_00039698:exon-1;Name=1:TCONS_00039698;Parent=1:TCONS_00039698;Target=1:TCONS_00039698 121525597 121526235 +;<o:p></o:p></p><p class=MsoNormal>scaffold_56 Cufflinks match_part 253262 253362 . + . ID=1:TCONS_00039698:exon-2;Name=1:TCONS_00039698;Parent=1:TCONS_00039698;Target=1:TCONS_00039698 121526236 121526336 +; <o:p></o:p></p><p class=MsoNormal>….<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>All the prediction algorithms have been trained before running Maker. Meanwhile, we provided the protein homology evidence. By simply checking the run.log file, I couldn’t find any records that show how RNA-Seq got involved into the prediction process (no blastn or exonerate for est). Is there anything I missed so the RNA-Seq evidence didn’t include in the prediction? Do I need to turn the est2genome on, since I suspect this option is only used when the algorithms aren’t trained properly? Or, do we need to set the value of pcov_blastn and eval_blastn a bit lower?<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><o:p> </o:p></p><p class=MsoNormal>Regards,<o:p></o:p></p><p class=MsoNormal>Sean <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>