The spaceranger aggr pipelines output a summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. Any alerts issued by the pipeline are displayed at the top of the page, such as an indication that results or sequencing data are out-of-spec. Further information about alerts is provided in the troubleshooting documentation.
Summary view
The summary metrics of an aggr run describe various characteristics about the aggregation process such as how many spots have been retained in the aggregated data.
Click Summary in the top left corner to access the run summary view.
Click the in the top of each dashboard for more information on each metric.
The individual sample images are not generated. To view the quality of alignment, refer to the individual web_summary.html outputs from spaceranger count pipeline.
Gene Expression view
Click Gene Expression in the top left corner to access the automated secondary analysis results.
Click the in the top of each dashboard for more information on each metric.
This view for spaceranger aggr provides two main outputs:
A joint reduced-dimension projection of spots into a synthetic 2-D space (t-SNE) based on gene expression of the aggregated dataset. The left plot shows total UMIs detected while the right plot shows clustering. The type of clustering analysis is selectable from the dropdown in the upper right - change this to vary the type of clustering and/or number of clusters that are assigned to the data.
A table at the bottom which shows genes that are differentially expressed in each cluster relative to all other clusters
