Compare multiple analyses and download a TSV file

You can compare multiple analyses, filter the variants that appear in the visualizations of the compared analyses, and download the collective results of the multiple analyses in a TSV file. Comparisons can be used to analyze results and identify common or unique hotspots of interest across analyses. TSV files that contain the results of multiple analyses can be downloaded separately or in a batch download that also includes VCF result files for each individual analysis. To download a TSV file from the IRGV & Generate Report tab, RNA Exon Variant tab, or TMB tab, you must download the TSV file in a folder of files. For more information, see Variants file downloads.

When you compare analysis results from one, two, or three similar analyses, the software generates a Venn diagram to show the sets of variants that are common between the analysis results and the sets of variants that are not common between the selected analyses. You can use the Venn diagram to select the unique or common sets of variants to narrow and refine the list of variants that are displayed in the Variant Table.

Venn diagrams are generated in Ion Reporter™ Software for two or three sets of analysis results. For more information, see Venn diagram generation. Venn diagrams are not generated for Ion AmpliSeq™ HD, Tagseq, immune repertoire, metagenomics, and microbiome analysis workflows, although you can make comparisons across similar analysis results with these analysis workflows.

  1. In the Analysis tab, click Overview, then select multiple analyses.

    Note: You can use the filters above the Analyses table to view only analyses of interest. For more information, see Find analyses.

  2. Click Actions > Visualize in the Selected Analyses section. The Analysis Visualization screen opens to the TMB tab.
  3. Click the Variants Table tab. The table view shows side-by-side columns that list the variants for the analyses.
  4. Refine the list of variants in the Filter Options section:
    1. Click the number in the overlapping set of the Venn diagram or other set of interest.
    2. Click Filter to update the table to include only the selected variants.
    3. (Optional) Click Clear to deselect all variants and restore the list to include all variants.

      Note: You can hover over a sample name in the Venn diagram to see the full sample name and the analysis to which the sample belongs. The analysis name is listed in parentheses.

  5. (Optional) View the filtered results in other visualization screens. For example, click CNV Heat Map to view a visual representation of copy number variation for the refined variant list.
  6. To download the refined multianalysis results in a TSV file:
    1. Click Download > Current Results TSV.
    2. Click the Home tab, then click Notifications.
    3. Find the download file in the list, then click (Download).
    The TSV file that contains the refined list of variants is downloaded. The TSV file is a tab-separated list of the variants. It contains the data and columns presented in the same order shown in the Variants Table.
  7. (Optional) Click Clear to deselect all variants and restore the Variants Table to include all variants.

Note: Under rare circumstances, the TSV file results can be duplicated in the Variants Table results in the Amino acid and Coding columns. This happens when the variant is Ref in one analysis, and a NOCALL in the other analysis.

Clustering in CNV heat map For CNV heat maps, ploidy is used as the score for every gene-sample pair to generate the heat map. After that hierarchical clustering is conducted for clustering genes and samples within the heat map.

Related Topics
Parent topic: Visualize analysis results with Ion Reporter™ Software
Child Topics
Venn diagram generation