Sequence duplication in fastqc

Question

[rajdeepboral00]

I have sequence duplication in fastqc reports while analysing for paired end reads for doing RNASeq. Do I have to remove the duplicates before proceeding to alignment and count generation?

Answer 1

[GenoMax]

It would help you to read some of the excellent blog posts by FastQC authors here: https://sequencing.qcfail.com/software/fastqc/

With RNAseq you do not remove duplicates (unless you have unique molecular indexes (UMI). One expects RNA's to be present in multiple copies for some genes and these would show up as "duplicates".

[rajdeepboral00]

Thankyou for your response