I would like to ask the difference between strand-specific and not strand-specific dataset.
As far as I know, strand-specific data means that we know which strand the transcript is from.
I do not have biological background. Please confirm whether it is correct. If we have a transcript, which is from sense strand, when RNA-seq is producing reads, is that first the cDNA is synthesised. Then this cDNA is used for PCR to amplify the sample? Then the reads generated could be from both strands of the original DNA?
For strand-specific protocols, what is different?