Normalization strategies for comparing mapped reads across samples in RNA-seq

Question

[Picasa]

Hi,

I have RNA-seq data from various samples under different conditions, and I'm interested in examining the mapping rate within the centromere and other regions. My plan is to map my reads to the T2T genome using STAR and then extract the centromere region using Bedtools.

However, I'm uncertain about the next steps. Is there a normalization method for mapped reads that allows for comparison between samples? TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length.

Do you have any suggestions?

[Ram]

TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length.

Also because TPM cannot be compared across samples. It's a relative within-sample measure.