I want to know, is it possible to identify copy number variations from paired end RNA-seq data? if yes , how? and which tools to use?
What I have done till now is:
a) Executed mpileup on the bam file of paired end RNA-seq file.
b) Next I wanted to use varscan copynumber, but it requires normal_pileup and tumour pile-up. I only have pileup on my experimental data. Hence I cannot move forward or am I missing a trick here?