Commit 814673f8 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: e-values, -e/-E

parent e6ffb915
......@@ -382,6 +382,9 @@ the clone sequence and the V(D)J germline genes. The default values should work.
(meaning that V and J could overlap 10 bp). This is the default for VJ recombinations
(except when using a =germlines.data= file).
The e-value set by =-e= is also applied to the V/J designation.
The =-E= option further sets the e-value for the detection of D segments.
** Further clustering (experimental)
The following options are experimental and have no consequences on the =.vdj.fa= file,
......@@ -394,7 +397,7 @@ being +1 for a match and -4 for a mismatch). However, more distant reads can als
be clustered when there are more than 10 reads within the distance threshold.
This behaviour can be controlled with the =-N= option.
The =-E= option allows to specify a file for manually clustering two windows
The =-== option allows to specify a file for manually clustering two windows
considered as similar. Such a file may be automatically produced by vidjil
(=out/edges=), depending on the option provided. Only the two first columns
(separed by one space) are important to vidjil, they only consist of the
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment