What are the nucleotide sequences of the adapters required for trimming prior to the software analysis of the sequencing reads?
What are the nucleotide sequences of the adapters required for trimming prior to the software analysis of the sequencing reads?
The final cDNA library generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian carries Illumina TruSeq® HT (currently known as TruSeq CD) indexing primers. The nucleotide sequences of the TruSeq HT i5/i7 indexes are available in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian User Manual. The complete nucleotide sequences of the corresponding Illumina TruSeq HT adapters are available from Illumina.
After the demultiplexing of Illumina adapters, the only nontemplated nucleotides required to be trimmed prior to mapping are the 3 nt in Read2, as described in Appendix A of the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian User Manual. There are no additional adapter sequences in the final cDNA library. The N6 Random Primer carries an overlap with the Illumina adapter and anneals to the complementary sequence of the RNA template. The random hexamer sequence is part of the RNA template, while the overlap with the Illumina adapter will be demultiplexed as part of the Illumina indexing primer.