Should I remove PCR duplicates from my RNA-seq data?
The short and generalized answer to the question "Should I remove PCR duplicates from my RNA-seq data?" is in most cases NO. For some scenarios, de-duplification can be helpful, but only when using UMIs. Please see the details below.
The vast majority of RNA-seq data are analyzed without duplicate removal. Duplicate removal is not possible for single-read data (without UMIs).