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Commit 3ff643ca authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/user.md: a few words on clones without V(D)J recombinations

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......@@ -657,6 +657,21 @@ Once clones are selected, you can send their sequence to **IMGT/V-QUEST** and **
by clicking on the links just above the sequence panel (bottom left).
This opens another window/tab.
## Why do some clonotypes not have V(D)J designations?
In a first step, vidjil-algo detects and cluster clones that have significant similarities to both V and J regions.
In a second step, vidjil-algo designates V, (D), and J genes on the clones.
Sequences without V(D)J designations are the ones that successfully went through the first step but not through the second step.
Such sequences can be *actual clones* that need to be investigated, especially clones with unusual recombinations, such as translocations.
They can be also *spurious clones*: For example low-complexity sequences may share significant regions to low-complexity regions of V or J genes.
Such spurious clones may appear especially on large datasets
coming from full RNA-seq or whole-genome sequencing.
Once these clones as selected, you can send their sequences to **Blast** or to **IgBlast** and/or to share us these sequences
(with `help > get support`, see below) for further inspection.
## How is productivity computed? Why do I have some discrepancies with other software?
Vidjil-algo reports CDR3 as *productive* when they come from
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