[maker-devel] Filtering of ab initio gene models
Carson Holt
carsonhh at gmail.com
Sat Jun 7 14:11:43 MDT 2014
If you give input as pred_gff, set keep_preds=1, and then give MAKER EST
evidence to work with then MAKER will just pass_through the pred_gff data
you gave it with UTR added. Set correct_est_fusion=1 if your input contains
false merges across regions (common from mRNA-seq results). This will trim
overlapping UTR caused by the improperly merged EST evidence.
--Carson
From: Volker Brendel <vbrendel at indiana.edu>
Date: Friday, June 6, 2014 at 3:52 PM
To: Carson Holt <carsonhh at gmail.com>, Daniel Standage
<daniel.standage at gmail.com>
Cc: Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Filtering of ab initio gene models
Hi Carson,
is there a way of allowing MAKER to add UTRs to our external models
(supplied by the pred_gff or model_gff tag)? This seems to be one problem
we are running into. Our external models are high quality, but CDS only.
Thus their score gets knocked down relative to ab initio predictions with
added UTRs.
Daniel will have more questions/observations later with regard to
overlapping gene models (we definitely need to allow gene models to overlap
in the UTRs, because transcript evidence clearly shows such negative
intergenic spaces).
Thanks for all your help!
Volker
On 6/6/2014 11:39 AM, Carson Holt 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
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>>
>
>
>
>
--
Volker Brendel
Professor of Biology and Computer Science
Indiana University
Department of Biology & School of Informatics and Computing
Simon Hall 205C
212 South Hawthorne Drive
Bloomington, IN 47405-7003
Tel.: (812) 855-7074
http://brendelgroup.org/
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