[maker-devel] Txome annotation
Shane Brubaker
sbrubaker at solazyme.com
Wed Jan 16 11:26:12 MST 2013
Does anyone have a good suggestion for annotating transcriptomes? In particular calling ORFs (like the best ORF, not just a simple longest ORF) and doing functional annotation?
I am currently using cd-hit to try and get a representative transcript set, but I want somthing similar in the ORF space that attempts to call the best, and alternative, ORFs.
I am using AutoFact to do functional annotation, and it works, but I don't think it is under continued development.
Thanks,
Shane
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Today's Topics:
1. Transcriptome data to gene models (Sivaranjani Namasivayam)
2. Re: Transcriptome data to gene models (Daniel Ence)
3. Re: Transcriptome data to gene models (Fields, Christopher J)
4. Re: Transcriptome data to gene models (Barry Moore)
5. Re: Transcriptome data to gene models (Carson Holt)
----------------------------------------------------------------------
Message: 1
Date: Wed, 16 Jan 2013 16:16:27 +0000
From: Sivaranjani Namasivayam <ranjani at uga.edu>
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Transcriptome data to gene models
Message-ID:
<A21F03FBB429334EB4D450CC75E8CBF35AB26199 at CH1PRD0210MB384.namprd02.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors
But I find gene models are not generated for all transcripts only about half of them.
Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision?
Thanks,
Ranjani
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Message: 2
Date: Wed, 16 Jan 2013 17:19:13 +0000
From: Daniel Ence <dence at genetics.utah.edu>
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Transcriptome data to gene models
Message-ID:
<F2774D6F47BB9D449EEA8B0BF6679D9C50D4B9B1 at mxb2.hg.genetics.utah.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Ranjani,
Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with.
Thanks,
Daniel
Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu]
Sent: Wednesday, January 16, 2013 9:16 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] Transcriptome data to gene models
Hi,
I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors
But I find gene models are not generated for all transcripts only about half of them.
Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision?
Thanks,
Ranjani
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Message: 3
Date: Wed, 16 Jan 2013 17:24:08 +0000
From: "Fields, Christopher J" <cjfields at illinois.edu>
To: Daniel Ence <dence at genetics.utah.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Transcriptome data to gene models
Message-ID:
<118F034CF4C3EF48A96F86CE585B94BF69BF2CEF at CHIMBX5.ad.uillinois.edu>
Content-Type: text/plain; charset="iso-8859-1"
I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome.
Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)?
chris
On Jan 16, 2013, at 11:19 AM, Daniel Ence <dence at genetics.utah.edu>
wrote:
> Hi Ranjani,
>
> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with.
>
> Thanks,
> Daniel
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu]
> Sent: Wednesday, January 16, 2013 9:16 AM
> To: maker-devel at yandell-lab.org
> Subject: [maker-devel] Transcriptome data to gene models
>
> Hi,
>
> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors
> But I find gene models are not generated for all transcripts only about half of them.
>
> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision?
>
> Thanks,
> Ranjani
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
------------------------------
Message: 4
Date: Wed, 16 Jan 2013 10:07:57 -0800
From: Barry Moore <barry.moore at genetics.utah.edu>
To: Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Transcriptome data to gene models
Message-ID: <F95B186F-40F3-4F01-B960-814298724796 at genetics.utah.edu>
Content-Type: text/plain; charset="us-ascii"
Ranhani,
Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options:
single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'
Barry
On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote:
> I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome.
>
> Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)?
>
> chris
>
> On Jan 16, 2013, at 11:19 AM, Daniel Ence <dence at genetics.utah.edu>
> wrote:
>
>> Hi Ranjani,
>>
>> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with.
>>
>> Thanks,
>> Daniel
>>
>> Daniel Ence
>> Graduate Student
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu]
>> Sent: Wednesday, January 16, 2013 9:16 AM
>> To: maker-devel at yandell-lab.org
>> Subject: [maker-devel] Transcriptome data to gene models
>>
>> Hi,
>>
>> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors
>> But I find gene models are not generated for all transcripts only about half of them.
>>
>> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision?
>>
>> Thanks,
>> Ranjani
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543
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Message: 5
Date: Wed, 16 Jan 2013 13:16:15 -0500
From: Carson Holt <carsonhh at gmail.com>
To: Barry Moore <barry.moore at genetics.utah.edu>, Maker Mailing List
<maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Transcriptome data to gene models
Message-ID: <CD1C588C.17C56%carsonhh at gmail.com>
Content-Type: text/plain; charset="us-ascii"
Yes.
Change single_exon=0 to single_exon=1.
--Carson
From: Barry Moore <barry.moore at genetics.utah.edu>
Date: Wednesday, 16 January, 2013 1:07 PM
To: Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Transcriptome data to gene models
Ranhani,
Are the transcripts for which no annotation is created all single exon?
With any predictor (est2genome included) you need some physical alignment
evidence for Maker to promote it to an annotation. In the case of using
est2genome as the only predictor it's a bit odd to think of it that way
since Maker is using the same data to predict a model and as evidence to
support it. However by default Maker requires EITHER a spliced transcript
OR protein evidence to support the model before it becomes a Maker
annotation. Thus with only est2genome and no protein evidence you will
never annotate a single exon gene (by default). If this is indeed the case
for you, you may want to consider the use of the following options:
single_exon=0 #consider single exon EST evidence when generating
annotations, 1 = yes, 0 = no
single_length=250 #min length required for single exon ESTs if 'single_exon
is enabled'
Barry
On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote:
> I think he is annotating a genome, but only using an available transcriptome
> as evidence (no gene prediction, possibly no BLAST). Note he mentioned
> setting est2genome.
>
> Is it possible that this is due to est2genome and not MAKER (e.g. est2genome
> is mapping only half of your transcriptome data)?
>
> chris
>
> On Jan 16, 2013, at 11:19 AM, Daniel Ence <dence at genetics.utah.edu>
> wrote:
>
>> Hi Ranjani,
>>
>> Maker was designed to annotate genomes, not transcriptomes. Transcriptome
>> annotation is very different from genome annotation. I think probably some of
>> your transcripts are just too short maker to work with.
>>
>> Thanks,
>> Daniel
>>
>> Daniel Ence
>> Graduate Student
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> From: maker-devel-bounces at yandell-lab.org
>> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam
>> [ranjani at uga.edu]
>> Sent: Wednesday, January 16, 2013 9:16 AM
>> To: maker-devel at yandell-lab.org
>> Subject: [maker-devel] Transcriptome data to gene models
>>
>> Hi,
>>
>> I want to generate gene models for all my transcripts (based on just the
>> transcript evidence). To do this I set 'est2genome to gene models' attribute
>> to 1. I have disabled gene predictions from any another sources, that is, I
>> do not provide protein data and turned off all gene predictors
>> But I find gene models are not generated for all transcripts only about half
>> of them.
>>
>> Can you tell me how maker decides which transcripts to predict models for,
>> that is, how is it making this selective decision?
>>
>> Thanks,
>> Ranjani
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543
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