I read this thread about Which software do you use for RNA-seq data quality control?. But for lnc RNA-seq or miRNA-seq, what should we carefully plan in the steps of quality control and preoprocessing before we analyze the data?
I don't think that anything will be fundamentally different for ncRNAs. The only big difference there is one of annotation quality, at least in terms of lncRNA annotations, which aren't currently up to the same quality as mRNA (or even miRNA) annotations. So the difficult part is accurately calling novel lncRNAs, even that's what you have in mind. This is all assuming that you're using a well-annotated model organism, of course.