Does the difference in computational strategy fully explain the discrepancy between the two studies? To under-stand the underlying causes, we also compared the **data** quality of the two studies. For the eight TRMT6/61A sites detected by both studies, a medium of ∼1200 coverage was seen in the IP samples by Li et al. (2017) compared to less than dozens of reads by Safra and colleagues ( Fig. 2A). As for the TRMT6/61A and TSS sites that were missed by Safra et al. (2017), a median coverage of ∼50-100 was observed by Li et al. (2017) compared to less than 10 reads per site by Safra and colleagues (Fig. 2B). Then, what could explain the huge difference in useful reads ( Fig. 2A,B), despite the fact that the raw sequencing reads by Safra and colleagues and Li et al. (2017) are actually comparable (within twofold)? We find severe reads duplication and rRNA contamination in the **data** of Safra et al. (2017) (Fig. 2C), possibly explaining why their **data** barely covered the sites identified in Li et al. (2017). Between the Dimroth reaction used by Safra and colleagues and enzymatic demethylation used by Li and colleagues, we previously performed a side-by-side comparison and already showed that the Dimroth reaction causes significant RNA degradation (see Figure S2E in Li et al. 2017).