I'm using TCGA RNASeqV2 expression data. They used UCSC annotation for annotating isoforms. I need to map the isoforms IDs to the RefSeq IDs, but I was able to map only 20% of them.
For this reason, I need to know, which version of UCSC annotation used for annotating RNASeqV2 data at TCGA.
Would someone help me to figure it out ?