Nucleic acid encoding reactions

A method of analyzing nucleic acids in or associated with single particles, the method comprising:

• a) capturing particles in separate reaction volumes, such that a plurality of reaction volumes each comprise a single particle, wherein the separate reaction volumes are droplets in an emulsion;
• b) producing barcoded reaction products from nucleic acids in or associated with the single particle in each of the separate reaction volumes, wherein producing the reaction products comprises incorporating barcoded adaptor nucleotide sequences into the reaction products using a plurality of different single-stranded barcoded adaptor molecules for each separate reaction volume, wherein each adaptor molecule comprises:
• (i) a nucleotide sequence comprising a primer binding site, (ii) a degenerate tail sequence, and (iii) a barcode nucleotide sequence, wherein each plurality of different single-stranded barcoded adaptor molecules comprises the same barcode;
• c) pooling the barcoded reaction products;
• d) amplifying the barcoded reaction products using primers that bind the primer binding sites, to produce templates for bidirectional DNA sequencing;
• and
• e) sequencing the barcoded reaction products.