Vidjil – Analyzed human locus

The Vidjil web application is able to display multi-locus data, as long as this information is provided in the .vidjil file computed by the analysis program. Vidjil-algo currently analyzes the following locus, selecting the best locus for each read. The configuration of analyzed locus is done in the germline/homo-sapiens.g preset.

    complete recombinations   incomplete/special recombinations
  TRA Va-Ja    
  TRB Vb-(Db)-Jb TRB+ Db-Jb
  TRD Vd-(Dd)-Jd TRD+ Vd-Dd3, Dd2-(Dd)-Jd, Dd2-Dd3
      TRA+D Vd-(Dd)-Ja, Dd-Ja
  TRG Vg-Jg    
  IGH Vh-(Dh)-Jh IGH+ Dh-Jh
  IGL Vl-Jl    
  IGK Vk-Jk IGK+ Vk-KDE, INTRON-KDE
vidjil-algo option   -g germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGL,IGK   -g germline/homo-sapiens.g
server configuration   multi   multi+inc

The detection of complete recombinations is reliable and should work provided that the reads are long enough (especially the J region).

The detection of incomplete/special recombinaisons is more challenging and may fail in some cases. In particular, as D genes may be very short, detecting TRD+ (Dd2/Dd3) and IGH+ (Dh-Jh) recombinations require to have reads with fairly conserved D genes or up/downstream regions.

Finally, the -2 command line option and the multi+inc+xxx server configuration try to detect unexpected or chimeric recombinations between genes of different germlines or on different strands (such as PCR dimers or +V/-V recombinations). These recombinations, tagged as xxx, can be technological artefacts or unusual biological recombinations.

Author: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)

Created: 2018-01-29 Mon 13:47

Emacs 24.3.1 (Org mode 8.2.4)

Validate