I know this is a very basic question, but I tend to mix them always. I was wondering what reads Do I get at the end, when I run a paired-end directional (or stranded) library preparation protocol.
I know from here, that in a single-end directional protocol the reads I see in the fastq files are the original transcripts, which are in the genome. (as opposed to the un-directional protocol, where one can't say from which strand the reads is coming from)
But what is happening when I'm sequencing a paired-end directional protocol?
Which of the two reads from each pair is which?
Can I make these statements?
- When doing a single-end (SE) directional library, The reads I get in the fastq files are the original mRNA sequences.
When doing SE un-directional sequencing there is no way of telling if the reads I see in the fastq files are from the sense or anti-sense strand
When I have a paired-end sample done with directional library prep., R2 of my sample is the original mRNA molecule, while R1 is the anti-sense