Are Read Groups (@RG tags) important when using tools like STAR, Kallisto, and Salmon for alignment?
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10 months ago
' ▴ 290

I am trying to better understand the role of Read Groups when aligning samples to a genome with the said tools. However, I have noticed Kallisto for example doesn't even take this info into account.

What is the role of Read Groups when simply aligning RNA-Seq reads to a genome using STAR/Kallisto/Salmon? Is it crucial to have this information embedded into the BAM file? Or can it be done later after the alignment?

Would there be any potential problems that would arise if RG is not provided during alignment?

alignment rna-seq rg group read • 241 views
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Entering edit mode
10 months ago
ATpoint 68k

No, not at all. Some tools, especially variant callers make use of RGs, but none of the above tools require them and for common downstream you do not need them either.

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