A pipeline for mapping and counting RNA seq reads including concentration spike-ins. Reads can be mapped against databases of choice, e.g. for small RNA-seq against piRNA, miRNA, tRNA databases and against a spike-in sequence database. The pipeline contains fuctionality to remove the spike-in associated reads. It allows for parameterization of the filtering steps that are applied in the counting procedure for a specific RNA-species in the snakemake file with which the workflow is operated.