[maker-devel] Filtering of ab initio gene models

Fri Jun 6 10:56:38 MDT 2014

I got the e-mail.  Thanks for the test set.

Multiple ab initio predictors don't inform a single annotation, rather one
must be chosen from the pool of available models (I.e. it has to be SNAP or
Augustus, or GeneMark).  They all supply their own ab initio as well as hint
based prediction, and then the one with best evidence match (measured by
AED) is kept (it's like a competition that only one predictor can win).

If you want a consensus model instead, you can take MAKER results in GFF3
format and give them to Evidence Modeler (EVM).  The upcoming MAKER 3.0 is a
collaboration with the EVM group and will have this option, but for now
users can just split the MAKER GFF3 by evidence types and give it to EVM.
EVM then produces consensus models based on the GFF3 content.

--Carson

From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Friday, June 6, 2014 at 10:46 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>, Volker Brendel
<vbrendel at indiana.edu>
Subject:  Re: [maker-devel] Filtering of ab initio gene models

Good to know, thanks. If multiple ab initio predictors inform a single
annotation, how does Maker decide which one will be included in the gene's
ID?

Given your quick response just now, I wanted to confirm that you got the
message and data set I sent yesterday. I received an email saying the size
of my message required list admin approval to be distributed, but since you
were also a direct recipient of the email I didn't worry about it too much.

Thanks again!

--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University

On Fri, Jun 6, 2014 at 12:39 PM, Carson Holt <carsonhh at gmail.com> wrote:
> snap_masked-$seqid-processed-gene was produced by SNAP on the repeat masked
> sequence without hints (i.e. the ab initio call).
> maker-$seqid-snap-gene was produced by SNAP after receiving hints from MAKER.
> 
> In both cases MAKER is allowed to add UTR to the model (hence the 'processed'
> tag).
> 
> --Carson
> 
> 
> From:  Daniel Standage <daniel.standage at gmail.com>
> Date:  Friday, June 6, 2014 at 10:33 AM
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  Maker Mailing List <maker-devel at yandell-lab.org>, Volker Brendel
> <vbrendel at indiana.edu>
> 
> Subject:  Re: [maker-devel] Filtering of ab initio gene models
> 
> Another question: is there documentation anywhere for the naming conventions
> of the genes annotated by Maker? Of course it's easy to spot genes based on a
> particular ab initio gene predictor, as the names are in the IDs. But what is
> the significance of, say, "snap_masked-$seqid-processed-gene" in a gene ID vs
> "maker-$seqid-snap-gene"?
> 
> Thanks,
> Daniel
> 
> 
> --
> Daniel S. Standage
> Ph.D. Candidate
> Computational Genome Science Laboratory
> Indiana University
> 
> 
> On Thu, Jun 5, 2014 at 2:05 PM, Daniel Standage <daniel.standage at gmail.com>
> wrote:
>> I have attached data for a small 18kb region with a handful of genes, as well
>> as the corresponding maker_opts.ctl file. (This is a smaller and different
>> data set than what I was looking at yesterday, with a more well-defined
>> problem).
>> 
>> With the data files as is, Maker 2.31.3 reports a model from 4125 to 6400
>> with an AED of 0.23. If you exclude transcript TSA024184, Maker reports a
>> different gene from 6111 to 8345 with an AED of 0.01. Both of these genes
>> have transcript support: will Maker report overlapping genes under any
>> conditions? And even if Maker is forced to choose only a single gene to
>> report, why would the model from 4125 to 6400 ever be reported in place of
>> the one from 6111 to 8345, especially since this is provided in the model_gff
>> file?
>> 
>> Even when transcript TSA024184 is included, Maker 2.10 reports the
>> high-confidence gene from 611 to 8345.
>> 
>> Any light you could shed would be helpful. Thanks!
>> 
>> 
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Computational Genome Science Laboratory
>> Indiana University
>> 
>> 
>> On Wed, Jun 4, 2014 at 3:17 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>> Just eAED, but eAED can affects selection of ab initio results.  For example
>>> reading frame match of protein evidence which also affects whether evidence
>>> from single_exon=1 and genes with single_exon protein evidence get kept.
>>> There is also the assumption that your alignments in GFF3 are are correctly
>>> spliced (like BLAT does).  So giving blastn results as precomputed est_gff
>>> would create a lot of noise, since maker ignores blastn and is using it only
>>> to seed the polished exonerate alignments.
>>> 
>>> --Carson
>>> 
>>> 
>>> From:  Daniel Standage <daniel.standage at gmail.com>
>>> Date:  Wednesday, June 4, 2014 at 1:11 PM
>>> To:  Carson Holt <carsonhh at gmail.com>
>>> Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
>>> Subject:  Re: [maker-devel] Filtering of ab initio gene models
>>> 
>>> I do not provide Gap or Target attributes in the GFF3. Will this affect the
>>> AED as well, or just the eAED?
>>> 
>>> 
>>> --
>>> Daniel S. Standage
>>> Ph.D. Candidate
>>> Computational Genome Science Laboratory
>>> Indiana University
>>> 
>>> 
>>> On Wed, Jun 4, 2014 at 3:09 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>> Sure.  that would be helpful.  One question. Do you provide the Gap
>>>> attribute in your precomputed alignments?  Having or not having that
>>>> attribute affects the eAED score which takes reading frame into account,
>>>> and may cause some things to be kept that normally would be dropped,
>>>> because MAKER won't be able to take the points of mismatch of the alignment
>>>> into account (it just assumes match everywhere).
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> From:  Daniel Standage <daniel.standage at gmail.com>
>>>> Date:  Wednesday, June 4, 2014 at 1:03 PM
>>>> To:  Maker Mailing List <maker-devel at yandell-lab.org>
>>>> Subject:  [maker-devel] Filtering of ab initio gene models
>>>> 
>>>> Thanks everyone for your responses recently!
>>>> 
>>>> The reason for my recent flurry of email activity is that I'm seeing some
>>>> unexpected trends when running the new version of Maker with precomputed
>>>> alignments. Compared with an annotation I did a while ago (Maker 2.10,
>>>> Maker-computed alignments), this new annotation has a substantial number of
>>>> new genes annotated. If I compare distributions of AED scores between the
>>>> old and new annotation, it's clear that the new annotation has a lot more
>>>> low-quality models. If I look at new gene models that do not overlap with
>>>> any gene model from the old annotation, the likelihood that it's a
>>>> low-quality model is much higher.
>>>> 
>>>> I decided to run a little experiment. I annotated a scaffold first using
>>>> Maker 2.10 and then using Maker 2.31.3. I both cases, I used the same
>>>> pre-computed transcript and protein alignments and the same (latest)
>>>> version of SNAP as the only ab initio predictor. Maker 2.10 predicted 44
>>>> genes while Maker 2.31.3 predicted 63. If we group gene models into loci by
>>>> overlap, there are 33 loci with gene models from both 2.10 and 2.31.3, 1
>>>> locus with only models from 2.10, and 28 loci with only models from 2.31.3.
>>>> 
>>>> Before this experiment, I assumed the issue was related to providing
>>>> pre-computed alignments in GFF3 format and perhaps violating some important
>>>> assumption. However, this experiment makes me wonder whether there have
>>>> been changes to how Maker filters ab initio gene models between version
>>>> 2.10 and version 2.31.3? Do you have any ideas? If it would help, I could
>>>> put together a small data set that reproduces the behavior I just
>>>> described.
>>>> 
>>>> Thanks!
>>>> 
>>>> --
>>>> Daniel S. Standage
>>>> Ph.D. Candidate
>>>> Computational Genome Science Laboratory
>>>> Indiana University
>>>> _______________________________________________ maker-devel mailing list
>>>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/
>>>> maker-devel_yandell-lab.org
>>> 
>> 
> 

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