Hi all, I need some help analyzing RNA-seq data which has a list of differentially expressed genes. All expressed genes have values reported as FPKM. I need to predict the master transcription factor(s) that are driving the shift in transcriptome between the two conditions in my RNA-seq experiment. Help?
I've been trying to use Tetramer in Cytoscape for this, but every time I import the data, it says that it can't parse it and gives an error. I thought I formatted it correctly... 3 columns, A=gene name, B=FPKM in condition 1, C=FPKM in condition 2.
This is completely new for me. Any help is appreciated!