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Commit cd1ce22a authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/browser.org: Vidjil browser, user manual - draft

parent 69b9ae70
* 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
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