ft add-nucleosomes
ft add-nucleosomes adds nucleosome positions and MSP positions to the Fiber-seq bam. The input is a Fiber-seq bam file with m6A calls and the output is a Fiber-seq bam file with the nucleosome positions encoded in the ns and nl tags and the MSP positions encoded in the as and al tags.
It is usually unnecessary to run this command manually, as it is called by ft predict-m6a automatically. However, you can run it manually if you want to adjust the parameters of the nucleosome calling algorithm.