In a paired-end sequencing experiment, a mate pair is generated. Let's call them read 1 and read 2.
For this post, my question is with regards to the various forms of transcriptomic experiments.
When I split the fastq files into the two mates, does the mate 1 always corresponds to the 5' end and mate 2 to the 3' end of the fragment that is sequenced?
I am trying to differentiate between read pairs that came from the sense versus the antisense.