I'm having a bit of trouble finding out how to use fimo to discover TFBS. The questions I had were:
- How do you decide on good thresholds for PWM matching (--thresh)
- How much do the backgrounds matter, should these be calculated from the sequences you're submitting?
- Does how does Fimo handle masked fasta files? Is it better to submit hard of soft masked files?
Any other tips on good usage for this program would be much appreciated as I'm finding the documentation quite vague.