Question: unit scale in plotprofile plot - deeptools2
gravatar for sim.j.baum
11 days 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 • 68 views
ADD COMMENTlink modified 11 days ago by Devon Ryan92k • written 11 days ago by sim.j.baum50
gravatar for Devon Ryan
11 days ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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

ADD COMMENTlink written 11 days ago by Devon Ryan92k

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 11 days ago by sim.j.baum50

Yes, though I prefer RPGC for everything.

ADD REPLYlink written 10 days ago by Devon Ryan92k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1541 users visited in the last hour