[maker-devel] Transcriptome data to gene models

[Barry Moore]

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
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> 
> 
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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