[maker-devel] The est_gff option

[Sean.Li at csiro.au]

Hello,

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:

....
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 +;
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 +;
....

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?

Thanks!

Regards,
Sean



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