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Commit 16c5abab authored by Mikaël Salson's avatar Mikaël Salson

user.org: clone definition

parent ef909825
......@@ -257,6 +257,27 @@ The different permissions that can be attributed are:
- View Details: Permissions to view patient/run data in an unencrypted manner for the patients/runs of a group
- Save: Permissions to save an analysis for the patients/runs of a group
* How do you define a clone? How are gathered clones?
Each software has its own definition of what a clone is (or, more precisely
a clonotype). Knowing how clones are defined is important to be aware of the
potential biases that could affect your analysis.
In Vidjil sequences are gathered into a same clone as long as they share the
same 50bp DNA sequence around the CDR3 sequence.
In a first step, Vidjil has a quick heuristic which detects approximatively
where the CDR3 lies and extracts a 50bp nucleotide sequence centered on that
region. This region is called a window in Vidjil's algorithm. When two
sequences share the same window, they belong to the same clone. Therefore
in Vidjil clones are only defined based on the exact match of a long DNA
sequence. This explains why some little clones can be seen around larger
clones: they may be due to sequencing error that lead to different windows.
However those small differences can also be due to a real biological process
inside the cells. Therefore we let the user choose whether the clones should
be manually merged or not.
In MiXCR clones are defined based on the amino-acid CDR3 sequence, on the V
gene used and on the hypermutations.
* Can I see all the clones ?
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