How to tell if library generation for RNA-seq experiments are stranded vs not stranded I would like to use RNA-seq data from the NIH GEO database. How can I tell if library generation for the RNA-seq experiments are stranded vs not stranded?
If you already have a reference transcriptome assembly, then you may run the Salmon tool for quantification using your RNA-seq samples. It has an automated library type inference function (https://salmon.readthedocs.io/en/latest/salmon.html#what-s-this-libtype). It might help you to determine whether the libs are stranded or not.