Hi, I really can’t help you without more information to answer either of your questions (number of genes or the transcripts without AEDs). If you ran maker with some evidence to annotation those 23000 genes, then some of those genes were probably not supported
by the evidence. Did you give those 23000 genes as predictions or as models? Those are two different options in maker and would give different results.
I am so sorry that I can not expound my question for you. I run maker with a annotation file(gff) which has 23000 genes, but I got a result with only 21553 genes. Why there were fewer genes than original file? Thank you very much!
Do they have no AED or an AED value of 0. A value of 0 means a perfect match to the evidence.
Also make sure you are not looking for AED in the predictions (i.e. GFF3 source column snap/augustus that are of type match/match_part). Those are rejected models and will not have quality statistics calculated for them (they are only there as alignments for reference purposes).
Only models with the source column of ‘maker’ and a type of 'gene/mRNA/exon/CDS’ represent the gene models and will have AED and QI values.
You can force MAKER to also calculate quality statistics for rejected models by altering pred_stats in the maker_opts.ctl file.
pred_stats=0 #report AED and QI statistics for all predictions as well as models