Question: MAKER genome annotation results confusion
0
gravatar for imda
19 months ago by
imda10
imda10 wrote:

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.

ADD COMMENTlink modified 19 months ago by Juke344.0k • written 19 months ago by imda10
3
gravatar for Juke34
19 months ago by
Juke344.0k
Sweden
Juke344.0k wrote:

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.

ADD COMMENTlink written 19 months ago by Juke344.0k
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