Question: unit scale in plotprofile plot - deeptools2
gravatar for sim.j.baum
9 months ago by
sim.j.baum50 wrote:

Hi all,
I generated a plot via deeptools2 with the folliwing steps:

BamCoverage to generate a bigwig file from my bam file with default conditions plus --normalizeUsing RPKM
Next, i created a matrix at the regions of interest with computeMatrix and then used plotProfile to visualize this.

Here is my question:
What would be the unit scale on the y-axis?

I assume RPKM? However, I am not sure what underlying computation are done in the steps in between - and I am reluctant in using this. I looked in the literature where they used deeptools2 as well and there is a mix from r/bp, no unit at all, normalized reads, relative fold-enrichment, and seldom RPKM etc etc...

Maybe someone has experience with this? I think people from the deeptools developers are active here as well?
Thank you in advance.

deeptools2 chip-seq • 270 views
ADD COMMENTlink modified 9 months ago by Devon Ryan96k • written 9 months ago by sim.j.baum50
gravatar for Devon Ryan
9 months ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

The scale would be "RPKM-normalized coverage". There's no further scaling done once you've made your bigWig files.

ADD COMMENTlink written 9 months ago by Devon Ryan96k

Thank you. Its a related question, but could probably fill a seperate question: RPKM vs RPGC? Both normalization methods are fine to use in the work stream performed above?

ADD REPLYlink written 9 months ago by sim.j.baum50

Yes, though I prefer RPGC for everything.

ADD REPLYlink written 9 months ago by Devon Ryan96k
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