[maker-devel] maker snap output files

[Carson Holt]

There can also be hint based predictions.  They may be similar in size, but
there is no rule.  Generally maker.snap_masked.proteins.fasta will be
larger, as gene predictors tend to over predict (as much as 10 fold).  You
should always review your annotations in something like Apollo, to see how
the models compare to the evidence.  Just counts don’t really mean anything.

Thanks,
Carson

From:  dhivya arasappan <darasappan at gmail.com>
Date:  Tuesday, March 18, 2014 at 2:05 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: maker snap output files

Thanks Carson.

Is it normal that in my maker results after running snap, the number of
proteins (in *maker.proteins.fasta) Is actually less than the number of
proteins in my pre-snap maker results?  I assumed that annotations through
alignment+annotation through prediction would equal more annotations?

The unfiltered proteins file has more proteins though.

Thanks
Dhivya



On Mar 18, 2014, at 2:34 PM, Carson Holt <carsonhh at gmail.com> wrote:

> maker.proteins.fasta - these are the final filtered and modified protein
> models (this is what you want)
> maker.snap_masked.proteins.fasta - these are the raw unfiltered snap ab initio
> predictions (for reference purposes)
> maker.non_overlapping_ab_initio.proteins.fasta - these are non-redundant
> rejected models that do not overlap the maker.proteins.fasta entries. If you
> think you are missing a gene, look for it here.  Sometimes people use
> interproscan (very slow) to analyze this file for false negatives.
> 
> 
> These files are also described in the README distributed with MAKER in the
> “MAKER OUTPUT” section.
> 
> Thanks,
> Carson
> 
> 
> 
> 
> From:  dhivya arasappan <darasappan at gmail.com>
> Date:  Tuesday, March 18, 2014 at 1:27 PM
> To:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
> Subject:  maker snap output files
> 
> Hello,
> 
> I ran maker after running SNAP ab initio prediction (following instructions
> from the maker tutorial).  It ran successfully and when I ran fasta_merge, I
> got several output fasta files. I’m unable to find information on the tutorial
> about interpreting these different files. I’m hoping one of you can help.
> 
> *maker.proteins.fasta
> *maker.snap_masked.proteins.fasta
> *maker.non_overlapping_ab_initio.proteins.fasta
> 
> What is the difference among these? They all have different number of
> sequences.
> 
> Similarly,with transcripts:
> 
> maker.non_overlapping_ab_initio.transcripts.fasta
> maker.snap_masked.transcripts.fasta
> maker.transcripts.fasta
> 
> Thanks
> Dhivya
> 
> 



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