Commit e9a8f050 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/user.md: clustering, more details, link

parent 8a2360a5
......@@ -385,22 +385,30 @@ potential biases that could affect your analysis.
## How do you define a clone? How are gathered clones?
In vidjil-algo, called **vidjil-algo** (Giraud, Salson, BMC Genomics 2014),
Some RepSeq studies want to broadly cluster clones to have a global view on the immune repertoire.
One may want to focus on CDR3 on the amino-acid level, or on the nucleotide level.
One also generally wants to correct technological artifacts (PCR, sequencing).
On the contrary, when studying hypermutations in IGH recombinations,
people want to know as precisely as possible differences between sequences,
even when they occur for a single nucleotide in the V gene or elsewhere.
In **vidjil-algo** (Giraud, Salson, BMC Genomics 2014),
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, the algorithm 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 vijdil-algo. When two
sequences share the same window, they belong to the same clone. Therefore
in vidjil-algo clones are only defined based on the exact match of a long DNA
in vidjil-algo clones are only defined based on the (conservative) 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.
clones: They may be due to artifacts 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 clustered or not.
be manually clustered or not -- and the choice may depend on the purpose of her study.
In **MiXCR**, clones are defined based on the amino-acid CDR3 sequence, on the V
gene used and on the hypermutations.
Other software may have other definitions, see also [What is a clone ?](/vidjil-format/#what-is-a-clone).
## What is the sequence displayed for each clone ?
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