I am a undergraduate student assisting in cancer research. I am hoping to learn and become a better computational biologist.
I have tumor and matched normal RNA-seq samples from TCGA to call and annotate somatic variants. What more analysis do you think can be conducted next? What analysis can I conduct on the detected somatic variants? I should mention that I am trying to find mutation "patterns" across multiple cancer types.
I was also wondering in what direction I should expand from variant calling. I was considering differential gene expression but I would appreciate additional downstream analysis ideas.
Thank you very, very much for your time and help.