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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)