Question: Calculating nucleosome dyad densities
gravatar for mmmmcandrew
3.4 years ago by
mmmmcandrew70 wrote:

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.

ADD COMMENTlink written 3.4 years ago by mmmmcandrew70

You can use bamCoverage with the --MNase function first and then bigwigCompare the results to presumably end up with your desired bigWig track.

ADD REPLYlink written 3.4 years ago by Devon Ryan94k

Cool, thanks for the input. This is kind of where I was thinking of going. My only concern is that I would prefer to normalize the datasets and take the ratio first, but maybe this can't be helped.

ADD REPLYlink written 3.4 years ago by mmmmcandrew70

There's no way to go from bigWig->BAM, making a bigWig file is innately a lossy process. I would recommend that you do the following:

  1. Run bamCompare, but note the scale factors applied to each sample. You might need to use the --verbose option, I don't recall.
  2. Run bamCoverage --MNase on each sample to make bigWig files.
  3. Run bigwigCompare with the --scaleFactors set according to step 1. This should produce more or less exactly what you're trying to get (at least I suspect so).
ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Devon Ryan94k
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