Hi Azazel, you might want to check out tools from the Salzberg lab, in particular cufflinks, cuffdiff and cuffcompare:
I'm new to RNASeq data analysis as well, but those three tools do the kind of thing you seem to have in mind.
I'm new to RNASeq data analysis as well, but those three tools do the kind of thing you seem to have in mind.
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