Qusetion about the ab initio gene predictors result

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Qusetion about the ab initio gene predictors result

nanshan yang
Hi MAKER community :
I have questions about MAKER output files.I get result from ab initio gene predictors which use snap and augustus by maker,and after fasta_merge step,there are some fasta files as:
result.maker.augustus_masked.proteins.fasta
result.maker.augustus_masked.transcripts.fasta
result.maker.augustus.proteins.fasta
result.maker.augustus.transcripts.fasta
result.maker.non_overlapping_ab_initio.proteins.fasta
result.maker.non_overlapping_ab_initio.transcripts.fasta
result.maker.snap.proteins.fasta
result.maker.snap_masked..transcripts.fasta 
result.maker.snap_masked..proteins.fasta
result.maker.snap.transcripts.fasta 
result.maker.proteins.fasta
result.maker.transcripts.fasta
if i continue to analysis the fasta files,which fasta should i choose?
because i choose ab initio gene predictors,so the   result .maker.non_overlapping_ab_initio*fasta can be uesed into the downstream analysis?or the  result.maker.proteins.fasta
Thanks verymuch for any help or insights

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