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)

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
cloneDB occurrences x
cloneDB patients/runs/sets occurrences