I am currently trying to do differential gene expression with TCGA data imported with R (GDCquery). I want to utilize DESeq2 as it is widely used and want publication quality results. I am struggling to understand where "raw" counts are found for star - counts. Does anyone know if the "unstranded" column is truly raw counts, or is it RSEM data? I want raw data to work with for DESeq2. Please let me know about any of these questions.