I have general question.
Suppose I have two individuals. One is patient, other is normal. The defect in patient is loss of function of a gene (due to a very small deletion) which results in phenotype.
Surprisingly we also find some Mb duplication at maternal allele in chromosome 1. paternal chromosomes are normal.
In normal individual there is neither a small deletion nor a large duplication. Both paternal and maternal chromosomes are normal.
If we perform RNA-Seq, for these two individuals. Will the Normalization of raw counts follow usual method implemented in any available tools (DESeq2, edgeR or any other) or I have to take care of duplication and follow some other adjustments (which I don't know)?
We would like to perform differential expression analysis between patient and normal individual.
I hope the question is clear.
Please help if someone has a suggestion or prior experience.