Methods and compositions for nucleic acid sequencing

A method of preparing nucleic acids for analysis, the method comprising:

• providing a first index to nucleic acids in a plurality of first vessels to produce first indexed nucleic acids, wherein at least one of the first vessels comprises a plurality of cells or organelles containing chromatin and wherein the nucleic acids are from the cells or organelles, the first indexed nucleic acids comprising:
• a target nucleic acid,
• a transposon inserted into the target nucleic acid,
• an integration enzyme bound to the transposon, and
• the first index;
• combining the first indexed nucleic acids from the plurality of first vessels;
• distributing the combined first indexed nucleic acids among a plurality of second vessels such that a second vessel of the plurality of second vessels comprises the first indexed nucleic acids from multiple first vessels of the plurality of first vessels;
• adding a second index to the distributed first indexed nucleic acids to produce dual indexed nucleic acids in the plurality of second vessels;
• and
• combining the dual indexed nucleic acids.