MAKER genome annotation results confusion

Question

[imda]

Dear developers,

I am a little confused about my MAKER results, I got all these outputs:

merged_4.all.maker.augustus.proteins.fasta merged_4.all.maker.augustus.transcripts.fasta merged_4.all.maker.augustus_masked.proteins.fasta merged_4.all.maker.augustus_masked.transcripts.fasta merged_4.all.maker.non_overlapping_ab_initio.proteins.fasta merged_4.all.maker.non_overlapping_ab_initio.transcripts.fasta merged_4.all.maker.proteins.fasta merged_4.all.maker.transcripts.fasta

However, I do not know what is the real proteins and transcripts resulted from maker that I have to take to downstream analysis, because I have all augustus proteins.fasta and also I have other file that says all proteins.fasta?

I suppose that the files with the prefix "augustus" are those genes that were predicted by the software?

Thank you and best regards

Ivan.

Answer 1

[Juke34]

As explained in the tutorial , merged_4.all.maker.augustus.proteins.fasta are proteins predicted by augustus and merged_4.all.maker.proteins.fasta are the proteins from the gene models selected by MAKER. This last one corresponds to your annotation (maker.gff) and contains extra information like AED scores.