I have some small RNA seq data to analyze miRNAs . I trimmed the adaptors, selected reads of 18-25 nt, mapped the reads to the genome, detected novel and conserved miRNAs using mirdeep2. I’ve already done DE analysis and target predictions. However, I realized that I did not remove rRBAs, tRNAs, mRNAs, and other types of ncRNAs. I know I can filter them out using the Rfam and NCBI databese. But is it really a necessary step to filter them out? It will take me a long time to do these analysis.