Due to special mechanisms in creating CATS libraries such as template switching and artificial poly(A) tailing, particular trimming procedures are needed to clean the reads prior to mapping. This step is mandatory -- not completing or improperly completing this step may result in a low mapping rate of the reads.
Following commands (to download) are recommended to be used with the cutadapt software to trim reads prior to mapping. They are designed to be easy to use. They are based on the trimming tool cutadapt, so be sure it is installed on your computer before running the Diagenode trimming tools. We recommend cutadapt version 1.9 or higher. For the usage of cutadapt, please refer to the cutadapt user guide.