CNV Analysis for single bulk RNA-Seq Sample

Question

[hkarakurt]

Hello everyone,

I am analyzing CNV using bulk RNA-Seq data. I used Casper for this purporse since I need the regions of genes that CNV occurs (as I know RNASeqCNV does not provide this information).

But I am wondering if I do not have any control group and have single RNA-Seq sample, is it possible to use Casper or any other tool? Second, what if I create my own control group using publicly available data (multiple samples from multiple datasets from TCGA, GEO etc.). I thought if I collect lots of data to be control maybe tool can tolerate batch effect since it also uses BAF for analysis.

I am kind of stuck in this problem.

Thank you in advance.