Pipeline to analyse small RNAseq and tRNAs?
I have heard that the Small RNA Workbench from UEA can be an easy solution for a full small RNA pipeline.  It is java based, has a GUI, and is supposed to be easy to install and run.  I am not an expert in small RNA analysis, but I think this pipeline will certainly given you an idea about the steps needed for a small RNA analysis, it has been put together by experts.