Commit 58cbb1c4 authored by Marc Duez's avatar Marc Duez
parents a9a7ac2f 9860fafa
......@@ -144,6 +144,7 @@ Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all co
This allows in particular to select incomplete rearrangement using custom V or J repertoires with added sequences.
- The =-g germline/= option launches the analysis on the seven germlines, selecting the best locus for each read.
Using =-g germline/ -i= stests also some incomplete and unusual recombinations.
See [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]] for information on the analyzable locus.
Now the seed and window parameters are hard-coded for each germline. In a future release, the mechanism will be more flexible
and will parse the =germline/germlines.data= file.
......
......@@ -72,7 +72,7 @@ Otherwise, such =.vidjil= files can be obtained:
** The info panel (upper left panel)
- analysis :: name of the configuration file used for displaying the data
- locus :: germline used for analyzing the data. In case of multi-locus
data, you can select what locus should be displayed.
data, you can select what locus should be displayed (see [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]])
- sample :: name of the current point (you can change the selected point by clicking on
another point in the graph). The name can be edited (“edit”).
- date :: when the run was performed (edit either with “...”, or with the database, on the patient tab)
......@@ -253,6 +253,7 @@ There can be several causes leading to bad ratios:
- The data actually contains other germline/locus that what was searched for
(solution: relauch Vidjil, or ask that we relaunch Vidjil, with the correct germline sequences).
See [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]] for information on the analyzable locus.
- There are incomplete/exceptional recombinations
(Vidjil can process some of them, config =multi+inc= or command-line option =-i=).
......
#+TITLE: Vidjil -- Analyzed locus
#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Marc and Tatiana)
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/org-mode.css" />
#+OPTIONS: toc:nil
The Vidjil browser is able to display multi-locus data, as long as this information
is provided in the =.vidjil= file computed by the analysis program.
The Vidjil algorithm currently analyzes the following locus,
selecting the best locus for each read.
|----------------------+-------+-------------------------+--------+-----------------------------------|
| | | complete recombinations | | incomplete/special recombinations |
|----------------------+-------+-------------------------+--------+-----------------------------------|
| | *TRA* | Va-Ja | | |
| | *TRB* | Vb-(Db)-Jb | | |
| | *TRD* | Vd-(Dd)-Jd | *TRD+* | Vd-Dd3, Dd2-Jd, Dd2-Dd3 |
| | | | *VdJa* | Vd-(Dd)-Ja |
| | *TRG* | Vg-Jg | | |
|----------------------+-------+-------------------------+--------+-----------------------------------|
| | *IGH* | Vh-(Dh)-Jh | *IGH+* | Dh-Jh |
| | *IGL* | Vl-Jl | | |
| | *IGK* | Vk-Jk | *IGK+* | Vk-KDE, INTRON-KDE |
|----------------------+-------+-------------------------+--------+-----------------------------------|
| command-line option | | =-g germline= | | =-g germline -i= |
| 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.
/Development note./
The algorithm parameters are hard-coded for each locus, it is defined in the =algo/core/germline.cpp= files.
In a future release, the mechanism will be more flexible and will parse the =germline/germlines.data= file.
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