Commit 69f7c996 authored by Mikael Salson's avatar Mikael Salson Committed by Mathieu Giraud

user.md: Explains how productivity is computed and why there may have some discrepancies

parent 0ed1a657
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......@@ -321,7 +321,7 @@ The different permissions that can be attributed are:
- View Details: Permissions to view patient/run/set data in an unencrypted manner for the patients/runs/sets of a group
- Save: Permissions to save an analysis for the patients/runs/sets of a group
# How do you define clones, their sequences, and their V(D)J designation?
# How do you define clones, their sequences, their V(D)J designation and their productivity?
The Vidjil web application allows to run several RepSeq algorithms.
Each RepSeq algorithm (selected by « config », see above)
......@@ -377,6 +377,16 @@ 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.
## 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
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. Moreover IMGT/V-QUEST checks that there
is no stop codon only in the CDR3 and not in the full sequence.
# Can I see all the clones and all the reads ?
The interest of NGS/RepSeq studies is to provide a deep view of any
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