Detection of duplicated regions in RNA-seq data

Question

[Ankit]

Hi everyone,

Does anyone know the tool(s) to identify duplicates regions using RNA seq data of mouse?

I have RNA seq data of hybrid mouse cell lines. I expect that one allele has more than double expression in certain cluster/regions. That is it shows complete bias toward expression from one allele. I would like to identify these regions. Since I have aligned bam file of RNA seq data, is there a compatible tool which can detect it?

It will be very helpful if someone has suggestions.

Thanks

Ankit

[biofalconch]

It is a little bit confusing that you use genome terms trying to explain RNA-seq, but here is my take on it. Basically I think this could be solve doing a differential gene expression analysis, to see if expression of gene A is greater in condition X over condition Y. Then if you are looking for a specific gene just extract its results form the tables. More on the process of doing DGEA is here https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

[Ankit]

Yes, I used RNAseq because we don't have genome sequencing data for that hybrid cells. I did the DEG analysis already as you suggested and that was the source of information of possible duplication of one of the allele. I wanted to verify it using a tool (if any available) which is specifically designed for these tasks. Thanks