[maker-devel] maker snap output files

[dhivya arasappan]

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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