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vidjil
vidjil
Commits
56562513
Commit
56562513
authored
Apr 08, 2016
by
marc
Browse files
Merge branch 'dev' of
git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil
into dev
parents
9ffc238c
3ddaffb3
Changes
1
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Inline
Side-by-side
doc/format-analysis.org
View file @
56562513
...
...
@@ -55,8 +55,8 @@ Note that other elements could be added by some program (such as =tag= or =clust
"top": 1,
"seg":
{
"5": "TRGV5*01", "
5
start": 1, "
5end
": 86,
"3": "TRGJ1*02", "
3
start": 89, "
3end
": 118,
"5":
{"name":
"TRGV5*01", "start": 1, "
stop
": 86
}
,
"3":
{"name":
"TRGJ1*02", "start": 89, "
stop
": 118
}
,
"cdr3": { "start": 77, "stop": 104, "seq": "gccacctgggccttattataagaaactc" }
}
...
...
@@ -102,8 +102,8 @@ and 'IMGT clonotype (AA) or (nt)' could also be used by some programs).
"top": 1,
"seg":
{
"5": "TRGV5*01", "
5
start": 1, "
5
end": 86,
"3": "TRGJ1*02", "
3
start": 89, "
3
end": 118
"5":
{"name":
"TRGV5*01", "start": 1, "end": 86
}
,
"3":
{"name":
"TRGJ1*02", "start": 89, "end": 118
}
}
},
{
...
...
@@ -121,8 +121,8 @@ and 'IMGT clonotype (AA) or (nt)' could also be used by some programs).
"top": 3,
"seg":
{
"5start": 1, "
5end
": 100,
"3start": 101, "
3end
": 200
"5
": {"
start": 1, "
stop
": 100
}
,
"3
": {"
start": 101, "
stop
": 200
}
}
}
]
...
...
@@ -286,17 +286,17 @@ In the .analysis file, this section is intended to describe some specific clones
// names of V/D/J genes should match the ones in files referenced in germline/germline.data
// Positions must start at 1.
{
"5": "IGHV5*01",
"
5
start": 0,
"
5end
": 0,
"5":
{"name":
"IGHV5*01",
"start": 0,
"
stop
": 0
}
,
"4": "IGHD1*01",
"
4
start": 0,
"
4end
": 0,
"4":
{"name":
"IGHD1*01",
"start": 0,
"
stop
": 0
}
,
"3": "IGHJ3*02",
"
3
start": 0,
"
3end
": 0,
"3":
{"name":
"IGHJ3*02",
"start": 0,
"
stop
": 0
}
,
// any feature to be highligthed in the sequenc
// the optional "seq" element gives a sequence that corresponds to this feature
...
...
@@ -357,3 +357,22 @@ The default tag names are defined in [[../browser/js/vidjil-style.js]].
#+BEGIN_SRC js
"key" : "value" // "key" is the tag id from 0 to 7 and "value" is the custom tag name attributed
#+END_SRC
* Differences between programs
Due to specificities between programs, some elements may differ depending
on which program has been run.
** MiXCR
The output when using MiXCR differs from Vidjil on the id of each clone.
Where Vidjil provides the representative sequence of the clone, MiXCR
provides the representative sequence in =Amino Acids= followed by the name
of the =V gene= and the name of the =J gene=.
#+BEGIN_SRC js
{
"germline": ...
"id": CARPRDWNTYYYYGMDVW IGHV3-11*00 IGHJ6*00
...
}
#+END_SRC
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