Is there a recommended bioinformatics workflow for the xGen™ RNA Library Prep Kit?
Adaptase™ technology, used in the xGen™ RNA Library Prep Kit, adds a low complexity polynucleotide tail with a median length of 8 bases to the 3’ end of each fragment during the addition of the second NGS adapter molecule (Read 2 Stubby Adapter). Therefore, 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) data. We recommend using the STAR aligner (Dobin et al. 2013) as it is able to soft clip the synthetic tail sequence and provides efficient mapping without additional processing of your sequencing data.
For additional details, please refer to Appendix G: Data analysis and informatics in the xGen RNA Library Prep Kit Protocol.