I am involved in a Drosophila transcriptomics project in which we have been obtaining RNAseq data for microRNAs as well as mRNAs. In initial work we used CAP-miRSeq for the latter as the Tuxedo pipeline (used for the former) gave anomalous results for miRs. However we find that CAP-miRSeq can no longer find some dependencies it requires, and even when working it took an inordinate length of time to run. I wonder if anyone has experience of a more modern alternative that would preferably run on MacOS. My objective is to assign quantitive values of RPM to the set of microRNAs for the various tissues we are studying.