Review run results — Immune Response plugin

After your sequencing run completes, review the results in the Run Summary page.

In the Data tab, click Completed Runs & Reports, then search for your run.
Click the Report Name link to open the Run Summary for your run.
In the Run Summary , click the Plugin Summary link, or scroll down to the Plugin Summary tab.
The Plugin Summary lists any plugins that have completed analysis on your run.
Scroll down to the immuneResponseRNA section, then click the immuneResponseRNA.html link to open the immuneResponseRNA Report for all barcodes. Alternatively, click an individual barcode name to view the results for that barcode.

In the Analysis Summary, review your Mapped Reads, Valid Reads, and Targets detected by barcode.

Column	Description
Barcode Name	The barcode used for the sample.
Sample	Sample name as it was entered in the sequencing Run Plan.
Mapped Reads	Number of reads that map to the reference sequences.
Valid Reads	Percentage of mapped reads ≥50% amplicon length.
Targets ≥1 reads	Number of targets/genes with at least 1 read.
Targets ≥2 reads	Number of targets/genes with at least 2 reads.
Targets ≥10 reads	Number of targets/genes with at least 10 reads.

Scroll down then click the Sample Characteristics, Sample Correlation, Analysis of Selected Targets (only present if a Genes of interest subset .bed file was selected), or Analysis of All Targets tabs to review the data graphically.