Methods and systems for processing polynucleotides

A method of nucleic acid sequence analysis, comprising:

• (a) providing a plurality of partitions comprising a plurality of polynucleotide molecules and a plurality of barcode molecules, wherein:
• i. said plurality of partitions comprises at least 1,000 partitions;
• ii. said plurality of barcode molecules comprises at least 1,000 different nucleic acid barcode molecules having different barcode sequences;
• iii. said at least 1,000 different nucleic acid barcode molecules are disposed within separate partitions of said at least 1,000 partitions, such that each of said at least 1,000 partitions has a different barcode sequence of said different barcode sequences;
• and
• iv. said at least 1,000 partitions are at least 1% of said plurality of partitions;
• (b) subsequent to (a), generating a plurality of barcoded molecules from said plurality of polynucleotide molecules and said plurality of barcode molecules within said plurality of partitions;
• and
• (c) directing said plurality of barcoded molecules generated in (b) to nucleic acid sequencing, wherein a sequence of a given polynucleotide of said plurality of polynucleotide molecules is determined.