What Mapping Quality Read Should I Use For Down Stream Rna-Seq Analysis

Question

[Curiosity]

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

Answer 1

[Anna]

hi

I restrict my mapping quality (-q option in samtools) by 30. and it seems to work OK to me. Your option 4 looks the best from the ones you presented here. You def don't one none-unique reads in rna-seq!!

good luck

Anna

[Flies]

Don't you worry about under-representing similar genes (e.g. from gene duplication) when you require unique-mapped reads?

[K. Wyatt Mcmahon]

I'm also concerned about filtering out non-unique mapped reads. Can you explain why you choose to do this?