What should I consider when multiplexing samples?
What should I consider when multiplexing samples?
Any samples can be multiplexed. However, to get the best results, you should consider the following: *Fragment lengths from each sample must match. Libraries of different lengths will hybridize to the flow cell at different efficiencies, which can lead to uneven sample coverage. *All samples must use the same barcoding strategy (e.g., do not mix and match single-indexed samples with dual-indexed samples). *All samples must be barcoded with the same type of kit (e.g., you cannot mix TruSeq® barcoded samples with Nextera® barcoded samples). *Illumina-equivalent indexes must be known if using non-Illumina library prep kits. Alternately, you must know the index sequences and use them as a custom barcode.