Commit 7bab434b authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/: user documentation for unexpected recombinations 'xxx'

Thanks for @rchikhi for pointing this out.
parent 88d0f57e
......@@ -224,7 +224,7 @@ Locus/recombinations
This allows in particular to select incomplete rearrangement using custom V or J repertoires with added sequences.
- The =-g germline/= option launches the analysis on the seven germlines, selecting the best locus for each read.
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.
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.
A =germline/isotypes.data= file is provided to look for sequences with, on one side, IGHJ (or even IGHV) genes,
......
......@@ -225,8 +225,8 @@ Depending on your granted accesses, you can schedule a processing for a sequence
The processing can take a few seconds to a few hours, depending on the
software lauched, the options set in the config, the size of the sample and the server load.
The base configurations are « TRG », « IGH », « multi » (=-g germline=) and « multi+inc » (=-g germline -i=).
See also https://github.com/vidjil/vidjil/blob/master/doc/locus.org.
The base configurations are « TRG », « IGH », « multi » (=-g germline=), « multi+inc » (=-g germline -i=), « multi+inc+xxx » (=-g germline -i -2=, default advised configuration).
See https://github.com/vidjil/vidjil/blob/master/doc/locus.org for information on these configurations.
The « reload » button (bottom left) updates the status of the task, that should do =QUEUED= → =ASSIGNED= → =RUNNING= → =COMPLETED=.
It is possible to launch several process at the same time (some will wait in the =QUEUED= / =ASSIGNED= states), and also to launch process while you
......@@ -409,6 +409,7 @@ There can be several causes leading to bad ratios:
| =h=: IGH, IGH+ | |
| =l=: IGL | |
| =k=: IGK, IGK+ | |
| =x=: xxx | |
Note: You can select just one locus by holding the Shift key while pressing
the letter corresponding to the locus of interest.
......
......@@ -36,4 +36,5 @@ require to have reads with fairly conserved D genes or up/downstream regions.
Finally, the =-2= command line option and the =multi+inc+xxx= server configuration try to
detect unexpected or chimeric recombinations between genes of different germlines or on different
strands (such as +Vk/-Vk recombinations).
strands (such as +V/-V recombinations).
These recombinations, tagged as =xxx=, can be technological artefacts or unusual biological recombinations.
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