Starting from Rna-seq data raw counts, I used TCGAanalyze_Normalization function based on edger, so i obtained normalized count. If i perform same analysis on two data type (GRCh37 and GRCh38) i obtain completely different normalized counts.
Results are these:
If i look at two bam file (aligned against 37 ad aligned against 38), they showed the exactly amount of reads for each mentioned genes, so i think that problem is on normalization?
What are the differences?
Thanks in advance.