Why do I have reads that end in adapter sequences in my small RNA sequencing results?
Reads longer than the small RNA molecule will sequence into the adapter. For this reason, we recommend sequencing for only enough cycles to cover the small RNAs of interest, or trimming the later cycles before aligning. The sequence that would need to be trimmed from the 3' end is given here for reference.
This is the reverse complement of the index-specific primer sequence given in the Illumina Customer Sequence Letter, with the index sequence shown as nnnnnn.