Commit cefd98d4 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: -d for basic usage cases

parent 814673f8
......@@ -215,6 +215,7 @@ Germline databases (at least one -V/(-D)/-J, or -G, or -g option must be given f
A different 'germlines.data' file can also be provided with -g <file>
Locus/recombinations
-d try to detect several D (experimental)
-i try to detect incomplete/unusual recombinations (locus with '+', must be used with -g)
-2 try to detect unexpected recombinations (must be used with -g)
#+END_EXAMPLE
......@@ -644,10 +645,10 @@ require either the =-G germline/IGH= option, or the multi-germline =-g germline=
#+END_SRC
#+BEGIN_SRC sh
./vidjil -g germline -i -2 -3 data/reads.fasta
./vidjil -g germline -i -2 -3 -d 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.
# Assign the VDJ genes and try to detect the CDR3 of each clone.
# Assign the VDJ genes (including multiple D) and try to detect the CDR3 of each clone.
# Summary of clones is available both on stdout, in out/reads.vdj.fa and in out/reads.vidjil.
#+END_SRC
......@@ -685,8 +686,8 @@ This file will be relatively small (a few kB or MB) and can be taken again as an
#+END_SRC
#+BEGIN_SRC sh
./vidjil -c segment -G germline/IGH -3 data/segment_S22.fa
# Detailed V(D)J designation and CDR3 detection on all reads, without clone gathering
./vidjil -c segment -g germline -i -2 -3 -d data/segment_S22.fa
# Detailed V(D)J designation, including multiple D, and CDR3 detection on all reads, without clone gathering
# (this is slow and should only be used for testing, or on a small file)
#+END_SRC
......
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