Resolving spatial arrays using deconvolution

A method for identifying a location of an analyte in a biological sample, the method comprising:

• providing an array comprising a plurality of features on a substrate,
• wherein a feature of the plurality of features comprises:
• an oligonucleotide comprising a first spatial barcode;
• and
• a capture probe comprising a second spatial barcode and a capture domain;
• hybridizing a priming oligonucleotide to the oligonucleotide, wherein the priming oligonucleotide comprises a sequence that is substantially complementary to a portion of the oligonucleotide;
• extending the priming oligonucleotide using the oligonucleotide as a template, thereby generating an extended priming oligonucleotide;
• determining all or a portion of the sequence of the extended priming oligonucleotide and a location of the extended priming oligonucleotide;
• determining a sequence and a location of the first spatial barcode, and a location of the second spatial barcode based on the location of the first spatial barcode;
• associating the location of the extended priming oligonucleotide with the location of the first spatial barcode;
• capturing the analyte from the biological sample with the capture domain;
• and
• identifying the location of the analyte in the biological sample based on the location of the second spatial barcode.