Iso-Seq

Best primarily for projects looking to identify isoforms and structural variation in mRNA transcripts, this approach utilizes the long read technology of PacBio (click here for an in-depth discussion).  Although counts are part of this PCR free approach, it may not be the most cost effective approach for expression studies.  However, as every sequenced strand is a full transcript, Iso-Seq provides a robust assembly-free transcriptome that maintains alternative splicing information.

RNASeq

For many years, RNASeq was the primary approach for RNA expression studies and transcriptome assembly. Utilizing mainly short read technology (Illumina sequencing), RNASeq provides transcript fragments that can be quantified and compared for differences in expression.  Alternatively, they can be assembled to provide a rough transcriptome.  For researchers interested in alternative splicing, Iso-Seq is a more appropriate approach.