[maker-devel] maker-devel post from nanshangogo at gmail.com requires approval

[Carson Holt]

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, maker-devel-owner at yandell-lab.org wrote:
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> following mailing list posting:
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>    List:    maker-devel at yandell-lab.org
>    From:    nanshangogo at gmail.com
>    Subject: Qusetion about the ab initio gene predictors result
>    Reason:  Post by non-member to a members-only list
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> From: nanshan yang <nanshangogo at gmail.com>
> Subject: Qusetion about the ab initio gene predictors result
> Date: December 23, 2020 at 12:03:35 AM MST
> To: maker-devel at yandell-lab.org
> 
> 
> 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
> 
> 
> 
> From: maker-devel-request at yandell-lab.org
> Subject: confirm 102e4151023f6d0466a7c780132e8ca169e86aaa
> Date: December 23, 2020 at 12:03:58 AM MST
> 
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