Paired end reads and alternative splicing

[Kbautista]

Hello everyone,
Can anyone please explain how paired end reads can help to identify alternative splicing.
I am trying to decide whether to do single-end or paired-end RNA seq to investigate the differential expression and alternative splicing in mites.
Thank you

[nilshomer]

If one end maps to one exon, and the other end maps to another exon, you know they are on the same transcript. You can reconstruct the exon order by these joins. That is one way to use paired ends to get the alternative splicing without observing the splice junction directly.

[Kbautista]

Thank you, for the information.