Analysing and identifying miRNAs from RNA-seq data using miRDeep2 tool in Galaxy, a practical guide

Micro-RNAs (miRNAs) analysis from RNA-seq experiment data provides additional depth into the cellular gene regulation. Such analysis has been simplified using miRDeep2 tool available in freely accessible Galaxy Europe server and miRBase database that compiled the miRNAs in many organisms. Here, we are describing a step by step protocol on how to ultilised the tool and most importantly on how to prepared and compiled miRDeep2 results to be used for downstream analysis such as investigating the differential expression of the detected miRNAs. Currently miRDeep2 miRNAs count result output in the Galaxy are in the broken HTML page and processing such data are troublesome for further analysis unless the user setting up their software dependencies for the tool to run. Hence, we proposed a method to process this output so that it is usable for downstream processing without a single coding required.