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
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written
by
ziziqolo •
1 answer
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
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Please read the manual.
https://salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-mapping-based-mode