Detecting Aneuploidy from Bulk RNA-Seq Data

Question

[bioinfo1990]

Hello,

I have bulk RNA-seq data from a specific cell line (so it consists of one cell type), and I'm looking to identify aneuploidy. Are there any well-known tools that can take a BAM file or a count matrix and provide information on copy number variations across entire chromosomes or specific chromosomal regions? So far, most of the tools I've found are designed for DNA sequencing or single-cell RNA-seq.

Thank you for your help. I appreciate it!

[ATpoint]

a) I would doubt that the highly uneven coverage of RNA-seq allows for inference like that other than plotting count distribution of genes in a certain chromosome window versus the rest of the genome/transcriptome, and b) that's a great example of wrong use of OMICS. Aneuploidy can easily be detected in any cytogenetics lab. Just send an aliquot of the cell line to such a service and get results, thats 100x more reliable than this off-label OMICA mungins.