Question: Extract RPKM values from Diffbind
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gravatar for francesca3
3 months ago by
francesca330
francesca330 wrote:

Hi everyone, does anyone know if there is a way to extrapolate rpkm values from Diffbind?? Thanks Francesca

chip-seq diffbind rpkm • 159 views
ADD COMMENTlink modified 3 months ago by Rory Stark860 • written 3 months ago by francesca330
1
gravatar for Rory Stark
3 months ago by
Rory Stark860
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark860 wrote:

You can set the read score to DBA_SCORE_RPKM in dba.count(). You can do this when you originally count, or anytime after by calling

DBA <-  dba.count(DBA,peaks=NULL,score=DBA_SCORE_RPKM)

Then you can retrievethe RPKM values in a GRanges object (or data.frame):

rpkm <- dba.peakset(DBA, bRetrieve=TRUE)
ADD COMMENTlink written 3 months ago by Rory Stark860

Thank you Rory. I have another question. When I retrieve these RPKM values I obtain very low numbers (ranging from around 0.5 to 2). Which values should I expect for trusted regions? If I retrieve TMM values (DBA_SCORE_TMM_MINUS_FULL) these values range from around 10 to 200. Usually I was counting using DBA_SCORE_TMM_MINUS_FULL. Thank you.

ADD REPLYlink written 3 months ago by francesca330
1
gravatar for Rory Stark
3 months ago by
Rory Stark860
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark860 wrote:

RPKM values are much lower in general than read counts. The first step is to divide by how many million sequence reads you have in your library. So if you sequenced to a depth of 20M reads, all the counts would be divided by at least 20.

Here's how it's implemented in DiffBind:

rpkm    <- (counts/(width(intervals)/1000))/(libsize/1e+06)
ADD COMMENTlink written 3 months ago by Rory Stark860
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