I am involved in a Drosophila transcriptomics project in which we have RNAseq data for small RNAs (for microRNAs) in addition to total RNA (for mRNAs).
- The total RNA reads have been analysed satisfactorily using the Tuxedo pipeline using TopHat, Cufflinks, Cuffquant and Cuffdiff. (I run this locally on a fast desktop Mac.)
- Initially we applied the Tuxedo pipeline to the short RNA reads, but abandoned this because of an incidence (1 in 10) of anomalously low or high replicates that was inconsistent with the bigwig plots from the bam stage, displayed in the UCSC browser.
- We there switched to analysing the short RNA reads using the CAP-miRSeq pipeline on Unix, which initially — though very slow — gave consistent results. However recent attempts to process later samples by this method failed as the pipeline can no longer find some dependencies it requires.
I see no point in spending further time on either of these methods.
Has anyone experience of a more modern analysis method for microRNA RNAseq data, preferably one that would run on MacOS?
I have no trouble in running the Tuxedo pipeline and get good results with total RNA. The problem there is not my computer. Unless someone who has analysed microRNA using this package understands the problem I have encountered, there is no rationale basis for trying this again. As regards Cap-miRSeq, it does not run on the Mac, only on Unix. A colleague set it up on a virtual box. We are our support. Is there anyone working on RNAseq of microRNA?