Hi all- I would like to calculate nucleosome dyad densities from my MNase-seq data. Here is where things get complicated: I would first like to take the ratio of two normalized datasets, then calculate the dyad density from there. I have been successful in producing ratio files from two normalized datasets using deepTools bamCompare, but this can only generate BigWig or BedGraph files. I would now like to calculate dyad densities from those files. Is there a way this can be done? Are there alternative programs which would allow me to take the ratio of normalized datasets and produce a bam file as a ratio instead? Producing a BAM file would allow me to use deepTools bamCoverage "--MNase" option. Forgive me if this seems a stupid question, the concept of dyad density calculation is pretty foreign to me.
Question: Calculating nucleosome dyad densities
3.4 years ago by
mmmmcandrew • 70
mmmmcandrew • 70 wrote:
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