Bi-directional in situ analysis

A method for analyzing a sample, comprising:

• (a) contacting the sample with a plurality of detection probes, wherein:
• the sample comprises a nucleic acid comprising non-overlapping first and second regions of interest flanking an adaptor region that hybridizes to an anchor,
• each detection probe comprises an interrogatory region and a detectable label, and
• wherein the plurality of detection probes comprise detection probes labeled with different detectable labels, wherein the detectable label of each detection probe in the plurality of detection probes corresponds to a nucleotide or sequence in the interrogatory region of the respective detection probe;
• ligating a detection probe of the plurality of detection probes to the anchor to generate a ligation product, wherein the detection probe of the plurality of detection probes is complementary to the first region of interest;
• and
• detecting a signal associated with the detectable label of the ligation product;
• and
• (b) binding a polymerase to the other end of the anchor and incorporating a nucleotide and/or analog thereof into the anchor by the polymerase to generate an extended anchor (i) using the second region of interest as a template, or (ii) using a primary probe bound to the second region of interest as a template, wherein the primary probe comprises a region that hybridizes to the anchor.