To identify diverse post-transcriptional modifications of RNA molecules and determine the transcriptome-wide landscape of RNA modifications by means of next generation RNA sequencing, recently many studies have developed conventional or specialised sequencing methods. Examples of specialised methods are MeRIP-seq, m6A-seq, PA-mC-seq , methylation-iCLIP, m6A-CLIP, Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP and RiboMeth-seq). Many of these methods are based on specific capture of the RNA species containing the specific modification, for example through antibody binding coupled with sequencing of the captured reads. After the sequencing these reads are mapped against the whole transcriptome to see where they originate from. Generally with this kind of approach it is possible to see the location of the modifications together with possible identification of some consensus sequences that might help identification and mapping further on. One example of the specialize methods is PA-mC-seq. This method was further developed from PA-mA-seq method to identify mC modifications on mRNA instead of the original target N6-methyladenosine. The easy switch between different modifications as target is made possible with a simple change of the capturing antibody form m6A specific to mC specific. Application of these methods have identified various modifications (e.g. pseudouridine, mA, m5C, 2′-O-Me) within coding genes and non-coding genes (e.g. tRNA, lncRNAs, microRNAs) at single nucleotide or very high resolution.