Methods for spatial analysis using RNA-templated ligation

A composition comprising:

• (a) a spatial array comprising a plurality of capture probes affixed to a substrate, wherein a capture probe of the plurality of capture probes comprises (i) a spatial barcode and (ii) a capture domain, wherein the spatial barcode comprises a sequence that provides a location of an analyte in a biological sample;
• (b) the biological sample placed on the spatial array, wherein the biological sample comprises the analyte;
• and
• (c) a first probe and a second probe that are ligated together, thereby generating a ligation product, wherein the first probe and the second probe each comprise a sequence that is substantially complementary to a sequence of the analyte, and wherein one of the first probe or the second probe comprises a capture probe capture domain that is hybridized to the capture domain of the capture probe on the spatial array.