I'm just trying to make a plot for particular genes (~200) showing the correlation, or lack thereof, between mRNA sequencing and ribosome footprinting. As I have it now, the data I got on mRNA sequencing from another lab is reported in RNA counts - thus, to my understanding, there is no normalization to gene length. The data I have analyzed by ribosome footprinting, using cufflinks, is reported in FPKM. Thus, if I try to plot the ~200 genes for these 2 methods, there may be an inherent bias since FPKM is normalized to gene length. How can I run cufflinks to get an appropriate comparison (i.e. how do I get cufflinks to spit out RNA counts rather than FPKM)?
Question: I have mRNA seq data from another lab that reports reads by RNA counts. How can I compare to my cufflinks data, which reports FPKM?
3.8 years ago by
aswartz85 • 20
aswartz85 • 20 wrote:
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