Hi, I am new to RNA-sequencing data and have one question regarding normalization.
I could download RNA-sequencing data in both read counts and rpkm. I thought I could use rpkm for eQTL analysis but little confused because there was this sentence on the following page of GTEx website.
"The RPKM values that are downloadable have not been normalized or corrected for any covariates." https://gtexportal.org/home/documentationPage#staticTextLabMethods
This means I should normalize rpkm or read counts before eQTL analysis?
Thanks for your help!