Hello, My lab has generated data using the CUT&RUN protocol. Unfortunately, Its single-end data. I tried the CUT&RUN tools and the henipipe tool. Both are for paired end data.
Any suggestion how I can analyse these data ? Any idea how to set the parameters in case I use the classical Trimmomatic and bowtie2 ? Any other pipelines to try ?
Thanks and Regards. (Loosing my mind)