Follow step-by-step instruction at MiroPipeline and use Glazov, EA, Cottee PA, Barris WC, Moore RJ et al. data published: A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008 Jun;18(6):957-64. PMID: 18469162

Using sra-toolkit of ncbi help link to process .sra file

It seems that the pipeline is too old to be worth tried out. At least, it provides a routine to process the miRBase .fa files.

Let’s follow the main steps and adapt it to new convention.