Commit 417d555c authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/browser.org: documenting the "top" filter

Thanks to a question from AF (Rennes)
parent 2ba0b27f
......@@ -44,8 +44,9 @@ Otherwise, such .vidjil files can be obtained:
- or with “file”/“import/export”, manually selecting a .vidjil file
There is always a “LIL-L2” 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 the processing step before
- 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 the processing step before.
See below ("Can I see all the clones ?").
- 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),
......@@ -154,7 +155,53 @@ Once the processing is finished, click on the button "see result" and
the browser will load the data of the processed files. The first click
on this button can take a few seconds.
* Assessing the quality of your data and of the analysis
* Can I see all the clones ?
The interest of NGS/Rep-Seq studies is to provide a deep view of any
V(D)J Repertoire. The underlying analysis software (such as Vidjil)
try to analyze as much reads as possible (see below 'Number of segmented reads').
One often wants to "see all clones", but a complete list is difficult
to see in itself. In a typical dataset with about 10^6 reads, even in
the presence of a dominant clone, there can be 10^4 or 10^5 different
clones detected.
** The "top" slider in the "filter" menu
The "top 10" clones are the clones that are in the first 10 ones
in *at least one* sample. As soon as one clone is in this "top 10"
list, it is displayed for every sample, even if its concentration is
very low in other samples.
Most of the time, a "top 10" is enough. The hidden clones are thus the
one that never reach the 10 first clones. With a default installation,
the slider can be set to display clones until the "top 100" on the grid
(and, on the graph, until "top 20").
However, in some cames, one may want to track some clones that are
never in the "top 100", as for example:
- a standard/spike with low concentration
- a clone in a MRD following of a patient without the diagnostic point
(Upcoming feature). If clone is "tagged" in the =.vidjil= or
in the =.analysis= file, it will always be shown even if it does not
meet the "top" filter.
** The "other" clone
This virtual clone in the clone list groups all clones that are hidden
(because of the "top" or because of hiding some tags). The sum of
ratios in the list of clones is always 100%: thus the "other" clone
changes when one use the "filter" menu.
Note that the ratios include the "other" clone: if a clone principal
is reported to have 10.54%, this 10.54% ratio relates to the number of
analyzed reads, including the hidden clones.
* How can I assess the quality of the data and the analysis ?
To make sure that the PCR, the sequencing and the Vidjil analysis went well, several elements can be controlled.
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