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Analysis axes⚓︎

Information computed on each clonotype are detailed on the clone information panel (🛈 button). They can be shown as axes on the grid view. Some of them can be shown as data columns in the aligner (‖ button) and used by the color by menu.

Basic axes⚓︎

  • size: Ratio of the number of reads of the clone to the total number of reads in the selected locus
  • size (other sample): Ratio of the number of reads of the clone to the total number of reads in the selected locus, on a second sample (applicable when there are several samples)

  • locus: Locus or recombination system, as detailed here

  • V/5' gene, D gene, J/3' gene: V, D, and J genes (or 5' and 3' segments for incomplete or special recombinations), regardless of the allele

  • V/5' allele, D allele, J/3' allele: Same as above, but taking into acount each allele

  • clone consensus length: Length of the consensus sequence

  • clone average read length: Average length of the reads belonging to each clone
  • primers: Length of the consensus sequence between primers (inclusive), possibly interpolated, see Working with primers)

  • clone consensus coverage: Ratio of the length of the clone consensus sequence to the median read length of the clone. Coverage between .85 and 1.0 (or more) are good values. See clone coverage

  • GC content: %GC content of the consensus sequence

  • number of samples: Number of samples sharing the clone

  • tag: Tag, as defined by the user with the ★ button in the list of clones

  • VIdentity IMGT: V identity (as computed by IMGT/V-QUEST, availabe when the clonotypes have been submited there)

  • V ratio: coverage ratio of germline sequence of V segment. A complete coverage return 1.

N-region / CDR3 analysis⚓︎

  • V/5' deletions in 3': Number of deleted nucleotides at the 3' side of the V/5' segment
  • J/3' deletions in 5': Number of deleted nucleotides at the 5' side of the J/3' segment

  • N length: N length, from the end of the V/5' segment to the start of the J/3' segment (excluded)

  • CDR3 length (nt): CDR3 length, in nucleotides, from Cys104 to Phe118/Trp118 (excluded)
  • productivity: Productivity as computed by vidjil-algo (no CDR3 detected, productive, or unproductive
  • productivity detailed: Same as above, but with further detail on the non-productivity cause: stop-codon, out-of-frame, no-{WP}GxG-pattern, following ERIC guidelines (Rosenquist et al., 2017).

  • productivity IMGT: roductivity (as computed by IMGT/V-QUEST, availabe when the clonotypes have been submited there)

Other axes⚓︎

These values require to have some setup on some instances of the server.

  • cloneDB occurrences: number of occurrences in cloneDB
  • cloneDB patients/runs/sets occurrences: "number of patients/runs/sets sharing clones in cloneDB

Availability of axes⚓︎

name axes (grid view) aligner color_by
V/5' gene x x
V/5 allele x
D gene x
D allele x
J/3' gene x x
J/3 allele x
clone consensus length x x
clone average read length x x
GC content x x
N length x x
CDR3 length (nt) x
productivity x x x
productivity detailed x x
productivity IMGT x x
VIdentity IMGT x x
tag x x
clone consensus coverage x
locus x x
size x x
size (other sample) x
number of samples x x
primers x x
V/5' deletions in 3' x
J/3' deletions in 5' x
V/5' length x
J/3' length x
V/5' ratio x
cloneDB occurrences x
cloneDB patients/runs/sets occurrences