Commit 5025eba1 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/user.md: productivity

hum, duplicated from vidjil-algo.md
parent cd266b12
......@@ -582,11 +582,13 @@ by clicking on the links just above the sequence panel (bottom left).
This opens another window/tab.
## How is productivity computed? Why do I have some discrepancies with other software?
Vidjil-algo computes the productivity by checking that the CDR3 comes from
an in-frame recombination and that there is no stop codon in the full
sequence.
The productivitiy as computed by Vidjil-algo may differ from what computes
Vidjil-algo reports CDR3 as *productive* when they come from
an in-frame recombination, the sequence does not contain any in-frame stop codons,
and, for IGH recombinations, when the FR4 begins with the `{WP}-GxG` pattern.
This follows the ERIC guidelines ([Rosenquist et al., 2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508071/)).
The productivity as computed by Vidjil-algo may differ from what computes
other software. For instance, as of September 2019, IMGT/V-QUEST removes by default
insertions and deletions from the sequences to compute the productivity, as it
considers them as sequencing errors.
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