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Commit 9e510e43 authored by Mikaël Salson's avatar Mikaël Salson
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Doc: Browser manual

Add some details
parent 07c65407
......@@ -33,69 +33,112 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
* The elements of the Vidjil browser
** The info panel (top left panel)
** The info panel (upper left panel)
- analysis :: name of the configuration file used for displaying the data
- system :: system used for analysing the data. In case of multisystem
data, you can select what system should be displayed.
- point :: name of the current point (you can change it by clicking on
another point in the graph)
- date :: when the run was performed (manually curated)
- segmented :: number of reads that contained enough meaningful informations, for that point
- total :: total number of reads for that point
** 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.
- Under the « star » button it is possible to normalise clone concentrations
according to this clone. You must specify the expected concentration in the
“expected size” textfield (e.g. 0.01 for 1%).
- The « i » button displays additional information on each clone
- The list can be sorted on V genes, J genes or concentrations. At the top of
the list you need to click respectively on “V sort”, “J sort” or “sort”.
The + and - allow respectively to un-merge or re-merge all clones that have
already been merged.
** The graph
- The gray zones at the bottom of the graph show, for each point, the resolution (1 read / 5 reads)
- The gray areas 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 you want to recover some hidden points, you need to drag them from the “+” mark to the graph.
- 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"
- 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 vertical gray area shows the current point, you can change that by clicking on another point.
** The plot view
** The scatterplot view
- The axis of the plot (by default « V gene » / « J gene ») can be changed
- The axes 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)
** The aligner (bottom panel)
- When several clones are selected (you can select clones by clicking on
them either in the list, the graph or the scatterplot, or by drawing a
rectangle around clones to be selected in the scatterplot view), you can
view their sequences in the aligner.
- Sequences can be aligned together to see how they differ or how similar
they are (“align” button). After aligning them a shaded background identifies
substitutions and a dash identifies indels.
- You can remove sequences from the aligner by clicking on their name (and
therefore, you unselect them)
- You can visualize results by IMGT/V-QUEST and IgBlast on the selected sequences, in another window, by clicking on the corresponding buttons.
- You can unselect all sequences by clicking on the background of the scatterplot
* Assessing the quality of your data and of the analysis
* Asserting the quality of your data and of the analysis
To assert that the PCR, the sequencing and the Vidjil analysis went well, several.
To make sure that the PCR, the sequencing and the Vidjil analysis went well, several elements can be controlled.
** Number of segmented reads
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
*** analysis or biological causes
- a system (for example TRG) was analyzed and the data actually contains other systems.
(solution: Relaunch Vidjil with other systems :NOTNOW:)
- there are incomplete/exceptional rearrangements
(Vidjil can process some of them)
- a system (for example TRG) was analyzed and the data actually contain other systems.
(solution: Relaunch Vidjil with other systems :NOTNOW:)
- there are too many hypersomatic mutations
(usually Vidjil can process mutations until 10% mutation rate... above that threshold, some sequences are lost)
- there are incomplete/exceptional rearrangements
(Vidjil can process some of them)
*** PCR or sequencing causes
- there are too many hypersomatic mutations
(usually Vidjil can process mutations until 10% mutation rate... above, some sequences are lost)
- the read length is too short, the reads do not span the junction zone
(Vidjil detects a “window” including the CDR3. By default this window is 40–60bp long, so the read needs be that long)
** PCR or sequencing causes
- In particular, for paired-end sequencing, one of the ends can lead to reads not fully containing the CDR3 region
(solution: ignore this end, or extend the read length)
- 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 )
- 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)
- 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)
** Control with standard/spike
- 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)
- If your sample included a standard/spike control, you should first
identify the main standard sequence (if that's not already done) and
specify its expected concentration (by clicking on the star button).
Then the data is normalized according to that sequence.
- You can (de)activate normalization in the settings menu.
** Steadiness verification
- When assessing different PCR primers, PCR enzymes, PCR cycles, one may want to see how regular the concentrations are among the points.
- When following a patient one may want to identify any clone that is emerging.
- To do so, you may want to change the color system, in the “color” menu
select “by abundance at selected timepoint”. The color ranges from red
(high concentration) to purple (low concentration) and allows to easily
spot on the graph any large change in concentration.
* Reference
If you use Vidjil for your research, please cite the following reference:
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