I am attempting to analyze sequencing from mouse and chicken samples in Seurat by following the multi-dataset integration vignette on the Seurat website: https://satijalab.org/seurat/v3.1/integration.html. In their example they use
FindIntegrationAnchors(object.list = reference.list, dims = 1:30) to find anchors for integrating human pancreatic samples from four different platforms. This results in many anchor features that are used in subsequent steps. However, I am attempting to recreate the analysis with mouse and chicken samples. In the
FindIntegrationAnchors step, only three anchors are returned, rendering the following steps unworkable. I assume given the greater disparity between mouse and chicken expression than between different human samples, that there will be fewer anchors, but is there a way to collect more? Seurat claims this workflow can work for different species. Has anyone had success with such an analysis?