[maker-devel] Transcriptome data to gene models

[Daniel Ence]

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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