[maker-devel] Transcriptome data to gene models

[Sivaranjani Namasivayam]

I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models.  I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models.
Thanks for the information!
________________________________
From: Carson Holt [carsonhh at gmail.com]
Sent: Wednesday, January 23, 2013 9:59 AM
To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Transcriptome data to gene models

est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else.  This is because most EST type alignments tend to be partial.  MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models.  MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1).  MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript.  Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated.  You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short.

Thanks,
Carson


From: Sivaranjani Namasivayam <ranjani at uga.edu<mailto:ranjani at uga.edu>>
Date: Wednesday, 16 January, 2013 9:16 AM
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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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