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