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Commit d6a92a70 authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/algo.org: help on -m/-M

Thanks to a question by Tim Xiaoming Hu.
parent 9d0c334c
......@@ -165,7 +165,15 @@ Window prediction
#+END_EXAMPLE
The =-s=, =-k=, =-m= and =-M= options are the options of the seed-based heuristic. A detailed
explanation can be found in the paper. These options are for advanced usage, the defaults values should work.
explanation can be found in the paper. /These options are for advanced usage, the defaults values should work./
The =-s= or =-k= option selects the seed used for the k-mer V/J affectation.
The =-m= / =-M= options control the minimum and maximum difference of positions between the last
conserved k-mer of V and the first conserved k-mer of J. As they may be some sequencing errors or mutations
compared to the germline genes, this is not the size of the junction (even without inserted nucleotides
in the N region, this difference of position can equal to 20 or 30, or even more, if there are some
errors or mutations at the end of V and and at the beginning of J). Note that is even possible to set =-m -10=
(meaning that V and J could overlap 10 bp). This is the default for TRG recombinations.
The =-w= option fixes the size of the "window" that is the main
identifier to gather clones. The default value (=-w 50=) was selected
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