Commit 8b92fd45 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: adds -2 to the basic examples

parent e8e32a46
......@@ -615,8 +615,8 @@ require either the =-G germline/IGH= option, or the multi-germline =-g germline=
#+END_SRC
#+BEGIN_SRC sh
./vidjil -g germline -i data/reads.fasta
# Detects for each read the best locus, including an analysis of incomplete/unusual recombinations
./vidjil -g germline -i -2 data/reads.fasta
# Detects for each read the best locus, including an analysis of incomplete/unusual and unexpected recombinations
# Gather the reads into clones, again based on windows overlapping the detected CDR3s.
# Summary of clones is available both on stdout, in out/reads.vdj.fa and in out/reads.vidjil.
#+END_SRC
......@@ -625,8 +625,8 @@ require either the =-G germline/IGH= option, or the multi-germline =-g germline=
** Basic usage: Whole RNA-Seq or capture datasets
#+BEGIN_SRC sh
./vidjil -g germline -i -U data/reads.fasta
# Detects for each read the best locus, including an analysis of incomplete/unusual recombinations
./vidjil -g germline -i -2 -U data/reads.fasta
# Detects for each read the best locus, including an analysis of incomplete/unusual and unexpected recombinations
# Gather the reads into clones, again based on windows overlapping the detected CDR3s.
# Summary of clones is available both on stdout, in out/reads.vdj.fa and in out/reads.vidjil.
# The out/reads.segmented.vdj.fa include all reads where a V(D)J recombination was found
......
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