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Adaptase™ technology, used in the xGen™ RNA Library Prep Kit, adds a low complexity polynucleotide tail with a median length of eight bases to the 3’ end of each fragment during the addition of the second NGS adapter molecule (Read 2 Stubby Adapter). Considering this, it is normal and expected to observe them at the beginning of Read 2 (R2).
When read length is close to fragment size, the tail may also be observed toward the end of Read 1 (R1). We recommend using the STAR aligner (Dobin et al. 2013) as it can soft clip the synthetic tail sequence and provides efficient mapping without additional processing of your sequencing data.
For more details, refer to Appendix G: Data analysis and informatics in the xGen RNA Library Prep Kit Protocol.