Entering edit mode
8.0 years ago
jolin0701-dy
▴
100
I followed this paper "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks" in Nature Protocol to analyze RNA seq data.
In this paper, it does not remove duplicate by SAMTOOLS or Piscard.
But in other pipelines, I saw people do it.
My question is when to remove duplicates and it is OK to follow the pipeline in this paper without removing duplicates?
I want to select the genes with differential expressions from RNA-Seq data.