Do mate 1 and mate 2 reads correspond to the 5' and 3' ends?

Question

[Koustav Pal]

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.

Answer 1

[GenoMax]

mate pair means something specific in high throughput sequencing and refers to long-insert paired-end reads.

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?

R1 is 5'-->3' read from top strand of the fragment being sequenced. R2 is 5'-->3' read from the bottom strand of the fragment being sequenced. Whether they come from the sense or antisense strand will be determined by the library type and the annotation of the gene.