Any one could suggest me a work flow published/ basic strategy to analyze differential level of noncoding RNA as well identification of novel noncoding RNA especially long noncoding ones. I have 100XPE Ribo-depleted data set.
You didn't give us much information on what your research question is or what organism you are studying. The workflows for small RNA identification can vary a lot depending on the question you are asking and the identification process is not trivial and often consists of many parts (i.e. looking for 21mers, 24mers, etc. etc.).