I want to use CDS expression of human genes curated in TCGA data.
In order to obtain CDS expression, I was thinking to calculate RPKM from level3 *.translated_to_genomic.exon.quantification.txt after excluding first and last exons. However, I realized that excluding the exons doesn't return 5' and 3' free CDS sequences. If any of you did this before, can you please show me how to do this?
Thanks in advance,