Which protocol should I follow, RTM or RTL? What are the differences and how do I choose?

The main difference between CORALL RTM and RTL is the reverse transcription chemistry, which influences the insert size of the final libraries.

The RTM Chemistry is perfectly suited for expression profiling and for low-quality RNA input, including FFPE samples.
When this chemistry is used, the expected average size of the library is approximately 350 bp.
The RTM chemistry enables time- and cost-effective single-read sequencing for expression profiling (recommended length: SR50 - 150). Paired-end sequencing is also compatible (recommended length: PE50-75).

The RTL Chemistry is optimized to obtain longer reads and is more suitable for applications like alternative splicing studies, detection of fusion transcripts, isoform identification, transcript annotation (including de novo assembly), and more.
When this chemistry is used, the expected average size of the library is approximately 550 bp.
The RTL chemistry is optimal for challenging applications requiring paired-end sequencing (recommended length: PE100 - 150), but is also compatible with single-read mode (recommended length: SR150).