The current pipeline setup is made for a protocol that has now been revised. I think a new protocol was generated by RIKEN, however I haven't worked with that yet, so I cannot say so much about that. The following steps are currently part of the pipeline: • FastQC with raw reads • Building a STAR index if necessary • Trimming of Enzyme binding site at 5'-end and linker at 3'-end (both are customizable) • Cut Artifacts (some sequencing artifacts that could be produced during the protocol - not sure if that's so important) • Another QC round • Alignment using STAR • Get CTSS • MultiQC • Paraclu?