In this chapter, we explain our experience in handling data after completion of CAGE sequencing reads and extraction of the tags. Procedures related to the extraction of the sequencing tags from the linkers, which depend on the design of the experiment. Linkers can also contain DNA barcodes that can be used to determine the original RNA source in case the samples are mixed. In this chapter we also describe strategies for extraction of CAGE tags from possible contaminating sequences. Additionally, we describe how to assess the quality of the libraries in terms of sequencing quality and to look for potential contamination of sequences that are not derive from RNAs.