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. 2016 Oct 27;4:e2619. doi: 10.7717/peerj.2619

Figure 1. Pipeline of the PAR-CLIP read simulator implemented in the PARA-suite.

Figure 1

Part A describes the process of generating the error profile and other parameters learned from a real PAR-CLIP dataset. Part B starts to generate reads mapping to RBP binding sites (clusters) on transcript regions from a given transcript database (e.g., Ensembl genes). In Part C, the pre-calculated profiles are used to introduce T–C conversions, sequencing errors, indels and base-calling quality scores to the defined reads.