References

Gupta, Namita T. and Vander Heiden, Jason A. and Uduman, Mohamed and Gadala-Maria, Daniel and Yaari, Gur and Kleinstein, Steven H. (2015). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. In Bioinformatics, 31 (20), pp. 3356–3358. [doi:10.1093/bioinformatics/btv359][Link]

In these tabs information on the clonal relation of transcripts can be found. To calculate clonal relation Change-O is used (Gupta et al, PMID: 26069265). Transcripts are considered clonally related if they have maximal three nucleotides difference in their CDR3 sequence and the same first V segment (as assigned by IMGT). Results are represented in a table format showing the clone size and the number of clones or sequences with this clone size. Change-O settings used are the nucleotide hamming distance substitution model with a complete distance of maximal three. For clonal assignment the first gene segments were used, and the distances were not normalized. In case of asymmetric distances, the minimal distance was used.

Overlap tab

This tab gives information on with which (sub)classe(s) each unique analyzed region (based on the exact nucleotide sequence of the analyzes region and the CDR3 nucleotide sequence) is found with. This gives information if the combination of the exact same nucleotide sequence of the analyzed region and the CDR3 sequence can be found in multiple (sub)classes.

Please note that this tab is based on all sequences before filter unique sequences and the remove duplicates based on filters are applied. In this table only sequences occuring more than once are included.