In epitranscriptomic sequencing, most methods focus on either (1) enrichment and purification of the modified RNA molecules before running on the RNA sequencer, or (2) improving or modifying bioinformatics analysis pipelines to call the modification peaks.  Most methods have been adapted and optimized for mRNA molecules, except for modified bisulfite sequencing for profiling 5-methylcytidine which was optimized for tRNAs and rRNAs.
There are seven major classes of chemical modifications found in RNA molecules: N-methyladenosine, 2-O-methylation, N6,2-O-dimethyladenosine, 5-methylcytidine, 5-hydroxylmethylcytidine, inosine, and pseudouridine. Various sequencing methods have been developed to profile each type of modification. The scale, resolution, sensitivity, and limitations associated with each method and the corresponding bioinformatics tools used will be discussed.