FAQ

(1) How to pick a pre-trained bias model?

Pick a pre-trained bias model closes in specs to the experiment you are performing.

(2) How to retrain a bias model? What is the intuition in choosing the hyperparameter for bias_threshold_factor?

Non peak regions used in bias model training are filtered based on The bias_threshold_factor which is used as follows. The regions with total counts greater than 0.1_quantile(total counts in peaks)*bias_threshold_factor are filtered out.

• If bias_threshold_factor is set to very low value you might filter out a lot of non-peak regions and the bias model might be sub-optimal.

• If bias_threshold_factor is set to very high you might include non-peak regions with high counts and this might lead to the bias model capturing cell-type specific motifs (which is not ideal as we want to regress out only the bias motifs effect and not cell-type specific motifs effect).