What Mapping Quality Read Should I Use For Down Stream Rna-Seq Analysis
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
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Anna
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Curiosity •
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Curiosity •
1 answer
I'm also concerned about filtering out non-unique mapped reads. Can you explain why you choose to do this?
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K. Wyatt Mcmahon •
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