How should I choose the barcodes for multiplexing?

In general, we recommend processing a minimum of 8 samples, using a complete set of eight Small RNA i7 Indices for multiplexing (e.g., SRi7001-7008). However, if fewer barcodes are required care should be taken to always use indices that give a well-balanced signal in both lasers (red and green channels) for each nucleotide position. All columns (1-12) and rows (A-H) fulfill these criteria.
The individual libraries within a lane should be mixed at an equimolar ratio to ensure this balance.
An evaluation tool to check the color balance of index subsets is available under Support Tools.
Dual indexing is currently not available for Small RNA-Seq libraries.