I have 119 million mapped reads (38 million unique (who has same start and end) reads). 66 million of them have mapping quality >0 (23 million unique reads).
Which file I should select for my downstream RNA-Seq analysis of the below and why? 1. All reads (119 m) 2. All unique reads (38 m) 3. All reads with a mapping quality >0 (66 m) 4. All unique reads with a mapping quality >0 (23 m)
Platform -SOLID,Single end Mapper - Bioscope