Gviz Coverage Plots

Question

[Researcher]

I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular region where the pattern of reads mapped to the reference genome are different between the two bam files but when I try the following code to plot trackplots with coverage, the resulting plot is not consistent with what I see in IGV. I am not very familiar with this, aren't I supposed to normalize the data as well? please help me.

txdb <-TxDb.Hsapiens.UCSC.hg38.knownGene
txTr <- GeneRegionTrack(txdb, chromosome = "chr1", 
                        start = 153561336,  end = 153561564)
dTrack <- DataTrack(range = bam.file, genome = "hg38", type = "l", 
                     name = "Coverage", window = -1, 
                     chromosome = "chr1")

dTrack0 <- DataTrack(range = bam.file.0, genome = "hg38", type = "l", 
                     name = "Coverage", window = -1, 
                     chromosome = "chr1", col="red")

plotTracks(c(dTrack,dTrack0, txTr), from = 153561357, to = 153561585)

[Ram]

Do not post on multiple fora just because you want a fast response, it's plain rude. At least point to the other post so we know you're asking on multiple fora.

Post on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21122/gviz-coverage-plots

[Researcher]

Sorry, I didn't know that posting it on another forum was rude but I really need help with this.

[Ram]

I understand that but stick to one place at least for a while and always link to other places you've posted (reasonable places, we don't need to see your reddit post if you're not comfortable sharing your reddit username, for example)