For total RNA and sometimes for enriched small RNA inputs, the final library can contain library inserts that are longer than the miRNA fraction.
The adapters can also ligate to other RNA types present in total RNA (e.g., tRNAs, piRNAs, mRNAs, snRNA, and ribosomal RNA), hence long library fragments (200 – 1,000 bp) should be removed to focus the sequencing depth on the miRNA fraction.
In addition, small RNA-Seq library preps from limited amounts of starting material may contain linker-linker artifacts (at 120 bp). We recommend the use of Lexogen's Purification Module with Magnetic Beads (Cat. No. 022) for this size selection. A bundled version of the Small RNA-Seq Library Prep Kit including Purification Module with Magnetic Beads (Cat. No. 058) is also available from Lexogen.
Protocol guidelines for bead-based purification of Small RNA-Seq libraries can be found in Appendix G of the Small RNA-Seq Library Prep Kit User Guide.