Hi . Im looking into a package in usegalaxy that can show my RNAseq data is stranded or unstranded.
in order to know if your RNAseq datasets are stranded or unstranded, you need to align it against the reference genome; you can use RNA STAR. Then by using the BAM/SAM Mapping Stats tool, you can infer it by comparing the number of reads which map to positive and negative strand.
after mapping, you can check strandness using the “Infer Experiment” function of the RSeQC package.
GTN tutorial help for determining strandedness. Even if putatively “known”, it is a good idea to check.