@ Harald Surowy; Thanks alot , its quite helpful.

Still I would suggest look for good workshop around.. Those will help you out a lot to break the initial inertia

R / Bioconductor software may be useful to your problem. it has many packages to analyze NGS data (alignment, differential expression, annotation,...etc.)

If you are teending a workshop, you may not become the master of analysis. But you would get to know about several common jergons and name of several toolkit. Once done, then if you have data in your hand, you may ask questions in several platforms like these. Hope this would workout for you.

Thanks every one...your answers are quite informative.