We've done RNA-seq on polysome fractionation samples across three different
genotypes. We collected Rnp (free mRNA's) and Polysome (actively
translating mRNA's) fractions as well as input mRNA from the samples before
fractionation.

The idea of collecting input is not only so that we can look at
transcriptional changes but to normalize to something that would be free of
the technical variation and RNA loss that polysome fractionation can
produce.

This is my current idea for a workflow:

Tophat/Bowtie => htseq-count => divide poly/rnp counts by input counts per
gene/feature => edgeR differences between genotypes across
polysome/rnp/input categories

My question is thus: Is there a way to tell edgeR to normalize to the
input? Am I mucking things up my manually normalizing the read counts
before giving them to edgeR?

Thanks.
Best,
Scott Daniel
Zarnescu Lab
MCB Ph.D. Program
University of Arizona

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