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Old 02-24-2012, 04:20 AM   #1
ChrisAU
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Default 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
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Old 02-25-2012, 02:52 PM   #2
RockChalkJayhawk
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Cufflinks should also report gene expression for you. Otherwise I would use mergeBed from BEDtools to build a consensus.
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Old 02-26-2012, 11:49 AM   #3
ChrisAU
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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.
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Old 02-26-2012, 10:38 PM   #4
arvid
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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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