Consensus gene model

ChrisAU · 02-24-2012, 05:20 AM

Hi all,

I have three different transcript annotations in gff format, two of them were generated by Cufflinks. Now I would like to build a consensus gene model out of the three. Do you have any suggestions, which programs are suited best for this task?

Thanks
Chris

RockChalkJayhawk · 02-25-2012, 03:52 PM

Cufflinks should also report gene expression for you. Otherwise I would use mergeBed from BEDtools to build a consensus.

ChrisAU · 02-26-2012, 12:49 PM

I have two gene models from Cufflinks and a third one. They are quite similar for the most part, however, in some regions the exon-intron structure differs. The objective is, to calculate the most probable gene model out of them. mergeBed just merges all structures, there's no validation of the predicted models involved.

arvid · 02-26-2012, 11:38 PM

You could try letting RSEM assign the original reads to the sequences of your candidate transcripts. It will fit the reads by a EM method and thus assign the reads to the transcripts in a way that fits the data... Afterwards you could drop the models with low read support.

If the differences are minimal, it will be difficult to verify the models computationally - I would go back to the lab and clone the transcripts.

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02-24-2012, 05:20 AM	#1
ChrisAU Junior Member Location: Tübingen Join Date: Jan 2012 Posts: 9	Consensus gene model Hi all, I have three different transcript annotations in gff format, two of them were generated by Cufflinks. Now I would like to build a consensus gene model out of the three. Do you have any suggestions, which programs are suited best for this task? Thanks Chris

02-25-2012, 03:52 PM	#2
RockChalkJayhawk Senior Member Location: Rochester, MN Join Date: Mar 2009 Posts: 191	Cufflinks should also report gene expression for you. Otherwise I would use mergeBed from BEDtools to build a consensus.

02-26-2012, 12:49 PM	#3
ChrisAU Junior Member Location: Tübingen Join Date: Jan 2012 Posts: 9	I have two gene models from Cufflinks and a third one. They are quite similar for the most part, however, in some regions the exon-intron structure differs. The objective is, to calculate the most probable gene model out of them. mergeBed just merges all structures, there's no validation of the predicted models involved.

02-26-2012, 11:38 PM	#4
arvid Senior Member Location: Berlin Join Date: Jul 2011 Posts: 156	You could try letting RSEM assign the original reads to the sequences of your candidate transcripts. It will fit the reads by a EM method and thus assign the reads to the transcripts in a way that fits the data... Afterwards you could drop the models with low read support. If the differences are minimal, it will be difficult to verify the models computationally - I would go back to the lab and clone the transcripts.