Commit 213a5067 authored by Mathieu Giraud's avatar Mathieu Giraud
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browser.org: typos, détails

parent c68f3ac0
* Vidjil -- Browser Manual * Vidjil -- Browser Manual
This is the help of the Vidjil browser : [[http://www.vidjil.org/browser]].
This help will be extended in a few months.
Further help can always be asked to contact@vidjil.org. We can also arrange phone or Skype meeting. 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) The Vidjil team (Mathieu, Mikaël and Marc)
** Requierements ** Requirements
The Vidjil browser runs in any modern browser. It has been successfully tested on the following platforms The Vidjil browser runs in any modern browser. It has been successfully tested on the following platforms
- Firefox version >= XX - Firefox version >= XX
...@@ -22,12 +23,12 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -22,12 +23,12 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
There is always a “sample/L2-LIL.data” dataset for demonstration purposes. 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”) - 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 The maximal number of clones that can be displayed depends on what has been run before
- Due to sequencing errors, there may be several clones corresponding to a real clone. - 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), - 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) - inspect the sequences in the lower panel (possibly using the “align” function),
- click on “merge” if you think that the clones should be merged. - and 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. Once several clones are merged, you can still visualize them by clicking on “+” in the list of clones.
...@@ -35,32 +36,33 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -35,32 +36,33 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
** The info panel (upper left panel) ** The info panel (upper left panel)
- analysis :: name of the configuration file used for displaying the data - analysis :: name of the configuration file used for displaying the data
- system :: system used for analysing the data. In case of multisystem - system :: system used for analyzing the data. In case of multi-system
data, you can select what system should be displayed. data, you can select what system should be displayed.
- point :: name of the current point (you can change it by clicking on - point :: name of the current point (you can change the selected point by clicking on
another point in the graph) another point in the graph). The name can be edited (“...” button).
- date :: when the run was performed (manually curated) - date :: when the run was performed (manually curated, with “...” button)
- segmented :: number of reads that contained enough meaningful informations, for that point - segmented :: number of reads where Vidjil found a CDR3, for that point.
See [[Number of segmented reads]] below.
- total :: total number of reads for that point - total :: total number of reads for that point
** The list of clones (left panel) ** The list of clones (left panel)
- You can assign other tags (and thus colors) to clones using the “star” button. - You can assign other tags (and thus colors) to clones using the “” button.
The “filter” menu allows to further filter clones by tags. The “filter” menu allows to further filter clones by tags.
- Under the “star” button it is possible to normalise clone concentrations - Under the “” button it is possible to normalize clone concentrations
according to this clone. You must specify the expected concentration in the according to this clone. You must specify the expected concentration in the
“expected size” textfield (e.g. 0.01 for 1%). “expected size” field (e.g. 0.01 for 1%). See [[Control with standard/spike]] below.
- The “i” button displays additional information on each clone - 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 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 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 The “+” and “-” allow respectively to un-merge or re-merge all clones that have
already been merged. already been merged.
** The graph ** The graph
- The gray areas 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. - 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. If you want to recover some hidden points, you need to drag them from the “+” mark to the graph.
...@@ -72,12 +74,12 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -72,12 +74,12 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
** The scatterplot view ** The scatterplot view
- The axes 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. - 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 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) to display the clones according to their N length (that is N1-D-N2 in the case of VDJ rearrangements)
** The aligner (bottom panel) ** The aligner (bottom panel)
- When several clones are selected (you can select clones by clicking on - When several clones are selected (you can select clones by clicking on
...@@ -88,16 +90,16 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -88,16 +90,16 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
they are (“align” button). After aligning them a shaded background identifies they are (“align” button). After aligning them a shaded background identifies
substitutions and a dash identifies indels. substitutions and a dash identifies indels.
- You can remove sequences from the aligner by clicking on their name (and - You can remove sequences from the aligner by clicking on their name (and
therefore, you unselect them) 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 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 - You can unselect all sequences by clicking on the background of the scatterplot.
* Assessing the quality of your data and of the analysis * Assessing the quality of your data and of the analysis
To make sure that the PCR, the sequencing and the Vidjil analysis went well, several elements can be controlled. To make sure that the PCR, the sequencing and the Vidjil analysis went well, several elements can be controlled.
** Number of segmented reads ** 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. A first control 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. 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: There can be several causes leading to bad ratios:
...@@ -105,7 +107,7 @@ There can be several causes leading to bad ratios: ...@@ -105,7 +107,7 @@ 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. - a system (for example TRG) was analyzed and the data actually contains other systems.
(solution: Relaunch Vidjil with other systems :NOTNOW:) (solution: ask that we relaunch Vidjil with other systems)
- there are incomplete/exceptional rearrangements - there are incomplete/exceptional rearrangements
(Vidjil can process some of them) (Vidjil can process some of them)
...@@ -127,8 +129,8 @@ There can be several causes leading to bad ratios: ...@@ -127,8 +129,8 @@ There can be several causes leading to bad ratios:
** Control with standard/spike ** Control with standard/spike
- If your sample included a standard/spike control, you should first - If your sample included a standard/spike control, you should first
identify the main standard sequence (if that's not already done) and identify the main standard sequence (if that is not already done) and
specify its expected concentration (by clicking on the star button). specify its expected concentration (by clicking on the “★” button).
Then the data is normalized according to that sequence. Then the data is normalized according to that sequence.
- You can (de)activate normalization in the settings menu. - You can (de)activate normalization in the settings menu.
...@@ -139,6 +141,7 @@ There can be several causes leading to bad ratios: ...@@ -139,6 +141,7 @@ There can be several causes leading to bad ratios:
select “by abundance at selected timepoint”. The color ranges from red select “by abundance at selected timepoint”. The color ranges from red
(high concentration) to purple (low concentration) and allows to easily (high concentration) to purple (low concentration) and allows to easily
spot on the graph any large change in concentration. spot on the graph any large change in concentration.
* Reference * Reference
If you use Vidjil for your research, please cite the following reference: If you use Vidjil for your research, please cite the following reference:
...@@ -148,3 +151,4 @@ Mathieu Giraud, Mikaël Salson, et al., ...@@ -148,3 +151,4 @@ Mathieu Giraud, Mikaël Salson, et al.,
BMC Genomics 2014, 15:409 BMC Genomics 2014, 15:409
http://dx.doi.org/10.1186/1471-2164-15-409 http://dx.doi.org/10.1186/1471-2164-15-409
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