How to compute the mono-nucleotide position specific frequency matrix and plot for it

Question

[Ashley]

enter link description here

The figure comes from the paper (Fig.1): https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000834

The x-axis represents for the dyad's location (the middle of nuclesome), while the y-axis represents for the probability of each base. For example, the red curve stands for the probability of T at each position that the range of position is from downstream 300bp to upstream 300bp. The x-axis values can be obtained from MNase-seq, could you give me some advice about y values?

Thanks for all your help. Any suggestion about this question would be greatly appreciated! Thank you so much.

Best wishes, Ashley

Answer 1

[Ashley]

In fact, I obtained the x-axis. However, I don't know how to construct the position specific frequency matrix (PSFM).

The details are as follows:

enter link description here

But I couldn't understand it's meaning.