Commit 3cf6250b authored by Mathieu Giraud's avatar Mathieu Giraud

doc/locus.md: converted from doc/locus.org + some details

parent f45a2761
# Analyzed human locus
The Vidjil web application displays 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` | | `-g germline/homo-sapiens.g` |
| | | `-g germline/homo-sapiens.g:IGH,IGL,IGK` | | |
| 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.
#+TITLE: Vidjil -- Analyzed human locus
#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />
#+OPTIONS: toc:nil
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.
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