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  • Differential expression from Transcript assembly

    I obtained two RNA-seq assemblies from a eukaryotic organism for which a reference sequence is not available. There is a reference sequence for a closely related organism though. Anyway, I followed the instructions on the http://trinityrnaseq.sourceforge.net...tream_analyses for doing differential expression but did not understand something.

    How does edgeR know the expression levels of a particular transcript in two different samples? Do the assembled transcript names follow some pattern?

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