* Identification of novel modified sites – BoMoC does not capture the modification directly but rather the mis-incorporation signature resulting from the modified base. Therefore, sites where modification status has not been previously established may be difficult to confirm the identity of the modification.
* Pre-mature termination of cDNA – Approximately, 10% of miRNA species characterized using OTTR experience prematurely terminated cDNA products. While these levels are low compared to common reverse transcriptase, some species carrying very bulky modifications may be challenging to capture with OTTR.
* Diversity in species used for benchmarking – To date, miRNA and tRNA pools have been characterized with OTTR. However, more validation, with diverse RNA  and DNA species will increase the potential applications of OTTR.