the hexamer count for hexamer i at position j. To find the expected Tn5 insertion frequency at each position relative to the motif given the Tn5 insertion bias (see above), we computed the matrix cross product between the hexamer frequency matrix M and the Tn5 insertion bias vector. Finally, the expected Tn5 insertion frequencies were normalized by dividing by the mean expected frequency in the 50-bp flanking regions (the regions 200 to 250 bp from the motif). To correct for Tn5 insertion bias we subtracted the expected Tn5 insertion frequencies from the observed Tn5 insertion frequencies at each position. This was performed using the Footprint function in Signac.
