Measuring Differential Gene Expression

[PratD]

Hi everybody,

I'm an intern working on RNAseq data.
I cleaned and aligned them on a referenced genome with STAR.
And i used RSEM to summarize the results and to obtain TPM and FPKM values.
My genome contain a lot of gene copy and i would like measure differential expression the two copy of a same gene.
My problem is that i can't use package like DESeq or edgeR cause they're made to measure differential expression in the same gene in two condition, or to measure differential expression of two gene in the same condition, which isn't my case cause i want to measure two copy of 1 gene (so they extremely similar, close to 100% identity) in the same condition.

This should be more similar to Allele Specific Expression, but I don't know how to use these methods since i don't have allele but 2 genes...

So my question is how could I measure a differential expression between my genes copies ?

Maybe my problem already exists but I didn't find something that could help me

Thanks for help !