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* Vidjil -- Browser Manual



Further help can always be asked to contact@vidjil.org. We can also arrange phone or Skype meeting.

The Vidjil team (Mathieu, Mikaël and Marc)

** Requierements

The Vidjil browser runs in any modern browser. It has been successfully tested on the following platforms
 - Firefox version >= XX
 - Chrome version >= XX
 - IE version >= XX
 - Opera version >= XX
 - Safari version >= XX

** First aid

- Go to the « file » menu to access your data.
  Your files are protected with your login and password.
  There is always a « sample/L2-LIL.data » dataset for demonstration purposes.

- You can change the number of displayed clones by moving the slider « number of clones » (menu « filter »)
  The maximal number of clones that can be displayed depends on what has been run before (by default, 200) XXX

- Due to sequencing errors, there may be several clones corresponding to a real clone. 
   - You can select several clones (for example those sharing a same V and a same J), 
   - inspect the sequences in the lower panel (possibly using the « align » function)
   - click on « merge » if you think that the clones should be merged. 
     Once several clones are merged, you can still visualize them by clicking on « + » in the list of clones.


* The elements of the Vidjil browser

** The info panel (top left panel)


** The list of clones (left panel)

- You can assign other tags (and thus colors) to clones using the « star » button.
  The « filter » menu allows to further filter clones by tags.

- The « i » button displays additional information on each clone


** The graph

- The gray zones at the bottom of the graph show, for each point, the resolution (1 read / 5 reads)

- You can reorder the points by dragging them, and hide some points by dragging them on the "+" mark at the right of the points

- If your dataset contains sampling dates (for example in a MRD setup), you can switch between point keys and dates in "settings > point key" 


** The plot view

- The axis of the plot (by default « V gene » / « J gene ») can be changed

- Some presets are available in the « analysis » menu.
  
  To segregate a set of clones sharing a same V and J, it is often useful
  to display the clones according to their 'N length' (that is N1-D-N2 in the cas of VDJ rearrangements)



* Asserting the quality of your data and of the analysis

To assert that the PCR, the sequencing and the Vidjil analysis went well, several.

A first way is to check the number of « segmented reads » in the info panel. For each point, this shows the number of reads where Vidjil found a CDR3. 
     
Ratios above 90% usually mean very good results. Smaller ratios, especially under 60%, often mean that something went wrong.
There can be several causes leading to bad ratios: 

** analysis or biological causes

  - a system (for example TRG) was analyzed and the data actually contain other systems.
     (solution: Relaunch Vidjil with other systems :NOTNOW:)

  - there are incomplete/exceptional rearrangements 
    (Vidjil can process some of them)

  - there are too many hypersomatic mutations
    (usually Vidjil can process mutations until 10% mutation rate... above, some sequences are lost)

** PCR or sequencing causes

  - the read length is too short, do the reads do not span the junction zone 
     (The Vidjil detects a "window" including the CDR3. By default this window is XX, so )

  - In particular, for paired-end sequencing, one of the ends can lead to too short reads
     (solution: ignore this end, or extend the read length)

  - There were too many PCR or sequencing errors
     (this can be asserted by inspecting the related clones, checking if there is a large dispersion around the main clone)
 

* Reference

If you use Vidjil for your research, please cite the following reference:

Mathieu Giraud, Mikaël Salson, et al.,
"Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing",
BMC Genomics 2014, 15:409 
http://dx.doi.org/10.1186/1471-2164-15-409