Commit 83038c6d authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/algo.org: update doc, homo-sapiens.germlines

parent 1d5ebc17
......@@ -228,9 +228,9 @@ Germline databases (at least one -V/(-D)/-J, or -G, or -g option must be given f
-D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components
-J <file> J germline multi-fasta file
-G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)
-g <path> multiple locus/germlines. In the path <path>, takes 'germlines.data' to select locus and parameters
Selecting '-g germline' processes TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations
A different 'germlines.data' file can also be provided with -g <file>
-g <path> multiple locus/germlines. In the path <path>, takes 'homo-sapiens.germlines' to select locus and parameters
Selecting '-g germline' processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations
Files different than 'homo-sapiens.germlines', for example for other species, can also be provided with -g <file>
Locus/recombinations
-d try to detect several D (experimental)
......@@ -245,14 +245,14 @@ Locus/recombinations
Using =-g germline/ -i= tests also some incomplete and unusual recombinations (locus with a =+= in their name),
and using =-g germline/ -i -2= further test unexpected recombinations (tagged as =xxx=).
See [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]] for information on the analyzable locus.
- Analyzed locus and parameters are configured through the =germline/germlines.data= file.
- Analyzed locus and parameters are configured through the =germline/homo-sapiens.germlines= file.
A =germline/isotypes.data= file is provided to look for sequences with, on one side, IGHJ (or even IGHV) genes,
and, on the other side, an IGH constant chain.
To select a custom set of TR or Ig locus, you may copy =germline/germlines.data= into a new file,
as for example =germline/custom-germlines.data=, and run Vidjil with =-g germline/custom-germlines.data -i -2=.
- Several =-g= options can be used, as for instance =-g germline -g germline/isotypes.data=.
To select a custom set of TR or Ig locus, you may copy =germline/homo-sapiens.germlines= into a new file,
as for example =germline/custom.germlines=, and run Vidjil with =-g germline/custom.germlines -i -2=.
- Several =-g= options can be used, as for instance =-g germline -g germline/isotypes.germlines=.
- One can use other germline sequences possibly by defining another
=germlines.data= file that would refer to an alternative germline set or by
=.germlines= file that would refer to an alternative germline set or by
overwriting the existing germline sequences (in the FASTA file).
** Main algorithm parameters
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