Stringtie -> ballgown: What normalization should be done on FPKM values?

Question

[njbernstein]

Hi all,

I used stringtie to quantify an rna experiment and then loaded that data into ballgown. The standard unit used by ballgown is FPKM, as such I'm wondering what between sample normalization could or should be done on this data. I'm mostly interested in more rarely occurring transcripts.

Best, Nick