What does the read counts in IGV indicate?

Question

[kousi31]

Hi all,

I converted the FPKM read counts obtained from Stringtie into TPM by following this link In R : setting function fpkm -

fpkmToTpm <- function(fpkm)
{
  exp(log(fpkm) - log(sum(fpkm)) + log(1e6))
}

setwd ("/DATA/TPM/")
In=read.table("file_t_data_FPKM", stringsAsFactors = F, row.names = 1, header = T)
Data <- data.frame(fpkm=In[,2])
In$TPM <- with(Data, fpkmToTpm(fpkm))
write.table(In, "file_TPM", append = FALSE, sep = "\t", row.names = TRUE, col.names = TRUE)

When I visualized the reads in IGV I found all samples had reads aligned even when the read counts are around zero.

Example loci with 9 replicates (early(E), mid(M) and late(L) lactation stages with 3 biological replicates in each stage).

            TID   E1      E2   E3       M1    M2      M3         L1   L2  L3   
 MSTRG.16476.18   0.0034 0.10 2.28     0.0040 0.0046 0.034     18.89 0.64 7.08

In this loci I could visualize read counts in all sample. When the expression in the Mid stage is almost nil.