[maker-devel] Conensus gene model

[Parul Kudtarkar]

Hi Carson,

Thanks. I have attached another contig which is 22 kb, with as many as 3
exons EST alignments. Could you please recommend additional training. We
are currently running maker on the entire contig set and eventually merge
all the gff3 contig predictions. The using suggested parameter/methods we
would like to get a consensus gene-set with minimal false
positives/negatives.

Thanks,
Parul

> The contig in question is really too small to get much out of it (only 5
kb).  There was only one single exon EST alignments and a couple of
predictions with no evidence support.  Anything smaller than 10 kb is
mostly useless for annotation purposes.  You would really need a few
100kb
> length or longer contigs to glean enough information for optimizing your
parameters.
>
> The general suggestions for any maker run are to use proteins from a
closely related organism or a couple of closely related organisms for
the
> protein= option in maker.  Also leave single_exon set to 0, except for
certain eukaryotes that have a bias for single exon transcripts (i.e.
some
> fungi and oomycetes).  And leave keep_preds set to 0 because ab initio
predictors tend to over-predict by a wide margin (lots of false
> positives).
>
> Additional training would really depend on what your other contigs look
like.  Do you have any large contigs?  I could look at one of those and
give suggestions but the provided contig is just too short to glean
much.
>
> Thanks,
> Carson
>
>
>
>
>
> On 12-10-15 1:41 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:
>
>>Hello,
>>Please advice on the aforementioned query?
>>Thanks,
>>Parul Kudtarkar
>>---------------------------- Original Message
>> ----------------------------
>>Subject: [maker-devel] Conensus gene model
>>From:    "Parul Kudtarkar" <parulk at caltech.edu>
>>Date:    Fri, October 12, 2012 2:46 pm
>>To:      maker-devel at yandell-lab.org
>>--------------------------------------------------------------------------
Hi,
>>We are using snap(training set[hmm file] generated using est,protein and
contig file), agustus,genemarkE(we ran it outside maker and have gff3
>> file
>>as input). The output that we get is combination of various
>>gene-predictors and evidences. I have attached sample result file. What
would you recommend to get consensus result set? Bootstrapping the
resulting gff3 file (rerunning maker)?
>>Thanks,
>>Parul Kudtarkar
>>--
>>Scientific Programmer
>>Center for Computational Regulatory Genomics
>>Beckman Institute,
>>California Institute of Technology
>>http://www.spbase.org_______________________________________________
maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org --
>>Scientific Programmer
>>Center for Computational Regulatory Genomics
>>Beckman Institute,
>>California Institute of Technology
>>http://www.spbase.org_______________________________________________
maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>


--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org

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