Hello, I have a brain cortex gene count file. I used gtex qtl portal to normalized these gene count file by inverse quantile normalization. I want to ask this pipeline generate normalized gene count for eqtl only? Can i use this pipeline to generate normalized counts for not eqtl, I just want to normalize it for samples? I tried to normalized my brain tissue gene count using deseq2 package. I noticed a difference between these two methods. First, I am not really using gtf or TPM files during deseq2. Why do we need gtf and TPM and vcf file during gtex eqtl normalization? Second, After normalization with deseq2 my samples are 255 whereas for inverse: its 205 Third: is there any major difference between using these two techniques and which one can give us better results? Thank you.
