I recently have performed a new genome annotation with EVM, thanks to ab initio predictions, RNA-Seq data and homology protein alignments. As there was an old annotation already, I wanted to analyze the AED score from both annotations, which takes into account their accuracy in comparison to the data I have (RNA-Seq, etc.).
But after performing all the steps provided by the MAKER tutorial for the new annotation, all genes show the same score: 1.00; which means that there is no evidence that supports this gene structure. This, obviously, is impossible, due to the fact that has been obtained by the same data is being compared. The only difference is that I didn't include the protein homology data because its format was giving problems to MAKER.
Any help or suggestion is really appreciated.
These are the steps I performed:
/home/juantxo/maker/bin/maker -CTL nano /home/juantxo/maker/bin/maker_opts.ctl #The proper parameters were changed (proteins were taken out due to problems) ./maker -RM_off -force 2> maker.error #Checking the output tail maker.error cd genome.maker.output/ && less genome_master_datastore_index.log #Collect the results from all individual contigs into genome wide annotations. ./gff3_merge -d genome.maker.output/genome_master_datastore_index.log genome.all.gff