Question: What Mapping Quality Read Should I Use For Down Stream Rna-Seq Analysis
3
gravatar for Curiosity
9.0 years ago by
Curiosity120
Curiosity120 wrote:

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

rna • 2.0k views
ADD COMMENTlink written 9.0 years ago by Curiosity120
1
gravatar for Anna
8.9 years ago by
Anna90
Anna90 wrote:

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

ADD COMMENTlink written 8.9 years ago by Anna90

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

ADD REPLYlink written 8.8 years ago by Flies100

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

ADD REPLYlink written 8.8 years ago by K. Wyatt Mcmahon50
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