Actually, you can do a lot of different bioinformatics analysis for NGS (ChIP-seq, RNA-seq, transcriptome sequencing, miRNA-seq, etc.). If you want to get an overview of all, or get a first/basic idea, of how it might work, these workshops are really nice. Nevertheless, my experience is, that it is always hard to apply the stuff you learn there in your own environment (different machines, different sequencing method/protocol, etc.).
To name one example: I went to one of these RNA-seq courses at EBI. It was great and I really learned a lot. But for the workshop, they used a small example set and mapped/analyzed the data using R. Back in my lab, I tried it and it was not possible for me to use the pipeline at all (my fastq-file was 5GB instead of 2MB and I used the human genome instead of bacteria). So, in the end, it cost me several more weeks to get things done.
What I want to say: These workshops are nice to get a first idea, but every NGS experiment looks completely different and has to be interpreted solely.
So, if you have some specific experiment you want to analyze, I recommend one-on-one training sessions. My company offers private trainings. In this training sessions, your data will be used as examples and the complete analysis will run on your machines. We will guide you through the complete process and you have the possibility to ask questions whenever you want. You decide, how the input looks like and how the output should look like. If your sample differs from the regular ones, we will show you how to solve this problem and get the best results out of it. And one of the main advantages is the possibility to choose the tools you want. We recommend you some, but if you want to use, e.g. a specific mapping algorithm, we will help you integrating it into your pipeline.
The main benefit of these one-on-one trainings is the possibility to directly start working after the course. You know, that it works on your machines (everything is already installed), you know how to treat and analyze the data and (based on experience) you will learn much more. In a one-on-one conversation people tend to be not so shy... ending in great discussions and ideas.