Compare TFBAs between two sequences

[jtlovell]

Hi there! I am hoping to compare the binding affinity of a transcription factor using a known pwm. Basically asking, "is this motif over-represented in one sequence relative to another?". Is there a way to do this with TFBSTools? If not, do you have any advice on accomplishing this analysis? I imagine there are permutation/bootstrap methods ... Thanks! John