What is the best approach to normalize exon read counts between samples ?

Question

[Adeler001]

Hello I'm trying to calculate the read count for each exon in one of my genes for 3 affected patients and 3 unaffected patients from my RNA-seq data . I'm trying to find the best way to normalize these read counts to factor in variance in exon read depth and exon length between patients. Would calculating the tpm or fpkm be the best way to do this so I can compare read counts of each exon between

Answer 1

[igor]

There are packages such as DEXSeq specifically for performing exon-level differential expression analysis: https://bioconductor.org/packages/release/bioc/html/DEXSeq.html