We generally do not recommend using CORALL mRNA-Seq for FFPE and degraded RNA input. Poly(A) selection is performed via oligo(dT) bead capture, which will lead to 5' regions not being captured for a large proportion of transcripts when degraded RNA is used as input. This ultimately affects accurate transcript abundance estimation, as transcript length is used as a basis for normalizing read counts.
For samples with RNA integrity or quality scores (RIN, RQN) below 8, we strongly recommend using ribosomal RNA depletion (e.g. using Lexogen's RiboCop rRNA Depletion Kits) prior to CORALL library preparation.
Additionally, RTL is not recommended for use with degraded / FFPE RNA samples. For RTL to work properly, intact input RNA is required.
Please follow the CORALL Total RNA-Seq V2 recommendations for FFPE and degraded samples.