I have analysed some RNA-Seq data using the DESeq2 protocol for analysis of time course experiments between two conditions (http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments).
Now I have collected samples for MNase-Seq under an identical experimental setup and want to compare how the nucleosome occupancy is affected between my 2 conditions during the time-course. I have the count of adjusted reads for summits (i.e nucleosomes) calculated using DANPOS. Is it correct to to apply the DESeq2 likelihood ratio test to the MNase-Seq data, in order to identify changes in occupancy between the two conditions during the time-course?
Can I use these values to build a counts matrix and calculate differential summit values during the time-course between the two conditions or is there other package more adequate for MNase-Seq time-course analysis?