[maker-devel] maker snap output files

[Carson Holt]

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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