[maker-devel] Transcriptome data to gene models

[Fields, Christopher J]

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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