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Commit c68f3ac0 authored by Mikaël Salson's avatar Mikaël Salson
Browse files

Doc: Uniformisation of quotes in manual

parent 9e510e43
...@@ -17,18 +17,18 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -17,18 +17,18 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
** First aid ** First aid
- Go to the « file » menu to access your data. - Go to the file menu to access your data.
Your files are protected with your login and password. Your files are protected with your login and password.
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 (by default, 200) XXX
- 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. - 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.
* The elements of the Vidjil browser * The elements of the Vidjil browser
...@@ -45,13 +45,13 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -45,13 +45,13 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
** 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 star 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 star button it is possible to normalise 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” textfield (e.g. 0.01 for 1%).
- 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”.
...@@ -62,19 +62,19 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -62,19 +62,19 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
- 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.
- 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 vertical gray area shows the current point, you can change that by clicking on another point.
** 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 cas of VDJ rearrangements)
...@@ -97,7 +97,7 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o ...@@ -97,7 +97,7 @@ The Vidjil browser runs in any modern browser. It has been successfully tested o
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 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. 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:
...@@ -144,7 +144,7 @@ There can be several causes leading to bad ratios: ...@@ -144,7 +144,7 @@ There can be several causes leading to bad ratios:
If you use Vidjil for your research, please cite the following reference: If you use Vidjil for your research, please cite the following reference:
Mathieu Giraud, Mikaël Salson, et al., Mathieu Giraud, Mikaël Salson, et al.,
"Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing", Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing,
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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