How can I find that a RNAseq data is stranded or un-stranded by usegalaxy tools?

Hi . Im looking into a package in usegalaxy that can show my RNAseq data is stranded or unstranded.

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Hi @sajjadg4,
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.

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Hi @sajjadg4,

after mapping, you can check strandness using the “Infer Experiment” function of the RSeQC package.

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GTN tutorial help for determining strandedness. Even if putatively “known”, it is a good idea to check.