[maker-devel] empty maker2zff output

[Carson Holt]

Set protein2genome=1.  Even then you may noir get many results, but on a
whole genome you should get a few hundred that match uniprot enough to make
an annotation directly from protein.

Then with maker2zff use the -n flag to turn off all filtering, otherwise you
won¹t get any results (too little evidence support).

For the example not working, it is because it has really long UTRs, and one
of the default filters was set slightly too high for the example in 2.28 for
it to give est2genome results, but SNAP should still produce results.  The
filter was brought back down in 2.29 and 2.30.

‹Carson


From:  mun hua <mh.tan85 at gmail.com>
Date:  Monday, December 2, 2013 at 12:18 AM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] empty maker2zff output

Hi,

I noticed that this empty output may be because I am only using SwissProt
protein sequences as evidence, because I do not have any EST or transcript
data generated for my organism.

My question is, how does one proceed to train and generate final annotation
starting with only the assembled genome sequence and UniProt/SwissProt
sequences?

Please advise.

Thanks very much.


On Mon, Dec 2, 2013 at 11:53 AM, mun hua <mh.tan85 at gmail.com> wrote:
> Hi
> 
> I'm trying to create training data for SNAP using the maker2zff script that
> comes with the maker package version 2.28.
> I'm having the same problem as mentioned in this post:
> https://groups.google.com/forum/#!searchin/maker-devel/maker2zff/maker-devel/_
> Pq65Fb761U/s826h5lSxnYJ
> My genome.ann and genome.dna files are empty, but no errors were printed.
> 
> Any advice on this?
> 
> Thanks.
> Mun Hua

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