I am a bit confused about the sequencing in paired end reads, single reads and mate paired reads.
I know the difference between the protocols and why matepairs map <---- -----> and they have a much longer distance between them.
When performing sequencing on single reads, we sequence till the second adapter, meaning till the end. So, we sequence the entire fragment. With paired end reads as well as with mate paired reads we know the fragment sizes from our fragmentation step and we define how long the reads are gone be. For instance, we stop sequencing when our read length,let say, is about 80pb.
From the very beginning we know that the fragments in ME protocol are larger, so if we sequence only 80 bases towards the fragment beginning points (biotin labels), we have a large distance between them. With the PE we sequence till the ends of the fragments but we stop at some point.
Why cannot we perform PE sequencing on large fragments (as we do with ME)? We will sequencing till the end of the fragments but we can stay stop after 80bases and at the end we will have the same distance as with ME.