Commit c779cdbc authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: productivity, start/stop

parent 6ec207d2
......@@ -496,11 +496,12 @@ as provided by `make germline`.
The CDR3/JUNCTION detection won't work with custom non-gapped V/J repertoires.
CDR3 are reported as *productive* when they come from an in-frame recombination
and when the full sequence does not contain any in-frame stop codons.
and when the sequence does not contain any in-frame stop codons.
Note that some other software only consider stop codons in the CDR3,
and may thus under-estimate non-productivity. Vidjil-algo looks for in-frame stop codons
on all the available sequence (and may sometimes over-estimate non-productivity when
the sequence contains intronic regions).
and may thus under-estimate non-productivity.
When the sequence is long enough to start before the start of the V gene
or to end after the end of the J gene, vidjil-algo do not consider these intronic sequences
in the productivity estimation.
The advanced `--analysis-cost` option sets the parameters used in the comparisons between
the clone sequence and the V(D)J germline genes. The default values should work.
......
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