Q: How is the fourth column calculated for the digested_short.bdg, digested_mono.bdg, digested_di.bdg, and digested_tri.bdg output files when using the the flag --digested.

[ijeomameremikwu]

I use --digested to get the signal tracks for the NFR (nucleosome free regions), mononucleosomal, dinucleosomal and trinucleosomal reads. Could you explain how that score fourth column is calculated? Is it proportional to the read depth?

Ex. output for a *di.bdg file.
chrX 156002482 156002497 0.00079
chrX 156002497 156002709 0.00078
chrX 156002709 156004422 0.00008
chrX 156004422 156004823 0.99454

[wcalicow]

Hi! May I ask how the --digested flag works? I tried using it with the latest version (1.2.10) but it didn't output any signal tracks. Thanks in advance for the help!