Filtering gene segments
In some cases, it may be desirable to restrict the gene segments to a subset of interest.
For instance, noise in the identified clonotypes can be reduced by filtering based on:
- Chain. This is useful when the data is targeted to a subset of chains.
- Segment type. This is useful when the D or C segment types are not relevant to the analysis. Note that the V and J segment types are required for clonotyping.
Additionally, depending on the final goal of the analysis, the following can be used:
- Allele. If the main aim is to observe general trends (e.g., overall V, D, J, and C segment usage), restrict to the main allele "1".
Retaining all alleles can be important when allele-specific effects (for e.g., population genetics, haplotyping, or personalized immunogenetics) are of interest. This may increase run time and may not add value for low-coverage data, but could introduce ambiguity in identifying the correct gene segment.
- Functionality. If the main aim is to characterize the functional immune response, as is often the case in clinical applications, restrict to "Functional" gene segments.
Non-functional gene segments are usually more relevant in basic research or population genetics applications that seek to characterize the complete immune repertoire or study immune gene evolution.
The subset of interest can be obtained by filtering the table view as needed and saving the resulting subset using the Create New Sequence List button. Alternatively, Filter on Custom Criteria can be used.