I have just started working on TCGA data, and I observed that the RNA-seq (HT-Seq counts) files also have the ENSEMBL gene ids for miRNAs, which means that the expression values of miRNA genes are also present in the RNA-seq files.(?)
So then why does TCGA have a separate miRNA quantification dataset (files ending with .mirbase.mirna.quantification)?
I am confused because I plan to find both the differentially expressed genes as well as miRNAs, and don't know which dataset to consider for DESeq2.
Please help! :(