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?
Please correct me if I am wrong. There are multiple protocols to produce strand-specific RNA-seq libraries. The basic process is like:
- Get the RNA;
- Get its cDNA;
- Somehow mark the cDNA as sense or antisense when amplifying (PCR?) (here comes the differences between different protocols);
- Then REMOVE all antisense (or sense) cDNAs;
- Read the reads from clean cDNA library.
The result is that, the reads from this RNA can be used to assemble the sense cDNA. And for not strand-specific libraries, using the reads would be able to assemble both the anti-sense and sense cDNA.
Am i right about this problem? Thanks.