Q: In the immunoSEQ software, the reads can be displayed as total, median, average, and unique. Can you explain what the median and average reads are?
A: For the V and J usage histograms, if you select Total, the height of a given bar in the histogram will reflect the sum of read counts for all TCRs that use that V and J combination. If you select unique, the height of the bar will be the total number of unique TCR rearrangements that use that V and J. Median and average take the set of rearrangements that use a particular V/J combination and calculate the average read count and median read count across this set. That will be the height of the bar.