Question

RNA-Seq lib type

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3.4 years ago

ziziqolo ▴ 10

Hi,

I just want to find out my RNA-Seq data's type, weather it's Stranded or non-Stranded. I read comments and manual about Salmon, but I don't know HOW? I didn't use Salmon before. So I can’t thank you enough if you help, How can I realize my data's type?

With respect

Stranded RNA-Seq non-Stranded • 1.3k views

ADD COMMENT • link updated 3.4 years ago by Istvan Albert 102k • written 3.4 years ago by ziziqolo ▴ 10

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Run salmon on a few million reads with --libType A and it will make a best guess.

ADD REPLY • link 3.4 years ago by ATpoint 85k

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Would you please tell me about whole command that I should use? Thank you

ADD REPLY • link 3.4 years ago by ziziqolo ▴ 10

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Please read the manual.

https://salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-mapping-based-mode

ADD REPLY • link 3.4 years ago by ATpoint 85k

score 0 · Answer 1 · 2021-07-13

You should understand your data first. Align a subset of your data, then view it via IGV and verify that it behaves the way it should.

The sense/antisense orientation of the reads ought to be immediately clear.

FWIW there is even "software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation"

https://github.com/NBISweden/GUESSmyLT

the README for the tool above has a comprehensive tutorial of what the different library types are and how they work