Re: maker-devel post from nanshangogo@gmail.com requires approval

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Re: maker-devel post from nanshangogo@gmail.com requires approval

Carson Holt-2
The result.maker.proteins.fasta and result.maker.transcripts.fasta files contain the filtered annotations, and the other files are for reference purposes (i.e. snap and augustus raw unfiltered output). The non_overlapping_ab_initio files contain non-redundant ab initio predictions that do not overlap a final annotation (maker file). They were called by a predictor but rejected for lack of support. If you wanted to look for a potential missing gene model, that is where it would be.

—Carson



On Dec 23, 2020, at 12:03 AM, [hidden email] wrote:

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   Subject: Qusetion about the ab initio gene predictors result
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From: nanshan yang <[hidden email]>
Subject: Qusetion about the ab initio gene predictors result
Date: December 23, 2020 at 12:03:35 AM MST


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



Subject: confirm 102e4151023f6d0466a7c780132e8ca169e86aaa
Date: December 23, 2020 at 12:03:58 AM MST


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