Log2 transformed bigWig not opening in IGV/exporting correctly

[alicekcassel]

When I try to export the log2 transformed bigWig file to IGV, I get no visual peaks and the [NaN-NaN] message (see screenshot).
My code:

newBigWig <- myBigWig
newBigWig <- log2(newBigWig)

export.bw(newBigWig,"log2bigWig.bw")

The rest of my code from the exercise so far in case the problem is earlier (all has worked so far through making geom_area plot):

#Friday lecture: starting with slides 4
#genomic scores
suppressPackageStartupMessages(library(rtracklayer))
suppressPackageStartupMessages(library(GenomicRanges))

importRegion <- GRanges(seqnames="chr1",ranges=IRanges(133040000,133149400))
mySelection <- BigWigSelection(importRegion)
myBigWig <- import.bw("data/ENCFF940MBK.bigWig",selection=mySelection,as="RleList")
myBigWig

theMax <- max(myBigWig$chr1[133040000:133149400])
theMax

theMin <- min(myBigWig$chr1[133040000:133149400])
theMin

library(ggplot2)

TStartSite <- seq(133131166-500,133131166+500)
TSSdf <- as.data.frame(myBigWig$chr1[TStartSite])
TSSdf$position <- TStartSite

ggplot(TSSdf,aes(x=position,y=value))+geom_area()+theme_minimal()

[rubyfroom]

I am having the same issue, thanks for posting!

[ThomasCarroll]

hi both,

When we have a bigWig over just portions of the genome it is struggling to find a suitable data range to display. This is further compounded by using log and producing inf values.

So by default IGV will look as you show.

We can fix the display in IGV by controlling the Data Range or setting it to autoscale once we are looking at the region of interest.

Zoom in to gene, change display settings to autoScale should get a graph as attached.

thanks,

tom