I 'm working on RNAseq data as well, where we have two samples (KO and WT) and three replicates for each, so in total 6. We are looking at the coverage of reads at 5' position. I would like to compare the performance of coverage of specific genes with IGV, however before that I have to normalize the data. I am thinking of trying TMM normalization, but I am confused how I have to treat replicates,
The edgeR package: calNormFactors(object, method=('TMM').....)
How do I represent an object here? as 6 column matrix ? Or would you advice any other normalization methods for this case?