Output from Compare Immune Repertoires tool
Two outputs can be generated by the tool:
- Clonotype Sample Comparison (
), containing the clonotypes from each sample, see Clonotype Sample Comparison for more details.
- Compare Immune Repertoires (CIR) report (
). A report containing comparisons of repertoire properties.
CIR Report
The report starts with the following section:
- Summary. A summary table showing, for each input, the total number of clonotyped fragments, as well as the clonotyped fragments from each chain type. A fragment represents one single read or a pair of reads.
The remaining information in the report is given per chain type and only for those chain types for which clonotypes have been identified for at least two of the inputs.
- Resolved clonotypes. If Resolve clonotypes with ambiguous segments and/or Resolve clonotypes without C segment have been checked, this section will contain a table with information about how many clonotypes have been resolved:
- The number of clonotypes, if any, for which segments have been disambiguated, for each segment type (V, D, J, and C).
- The number of clonotypes, if any, for which a C segment has been added.
- Diversity indices. A table showing the diversity metrics 'Observed diversity', 'Extrapolated diversity (chaoE)' and 'Extrapolated Shannon-Wiener index (chaoE)', see Output from the Immune Repertoire Analysis tool. Additionally, the table contains the diversity metric 'Interpolated to lowest sample diversity', showing an estimate of the diversity if all the inputs had the same number of clonotyped fragments as the input with the lowest number of clonotyped fragments.
- Scatter plots. If exactly two inputs are compared, this section will contain scatter plots with the clonotypes frequency in the two inputs. The Clonotype Sample Comparison () can display the scatter plot for any two inputs at a time, see Scatter Plot For sample Comparison for more details.
- Rarefaction. A plot with rarefaction curves, also known as species accumulation curve. See Rarefaction For Clonotype Sample Comparison for more details.
- CDR3 length. A table comparing CDR3 length summary statistics for the different inputs, across all chains. For each chain type, the CDR3 length distribution is also shown as a histogram, see CDR3 Lengths For Clonotype Sample Comparison for more details.
- V, D, J and C usage. Bar plots showing the V, D, J and C segment usage for each input. See Segment Usage For Clonotype Sample Comparison for more details.