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vidjil
vidjil
Commits
4d172810
Commit
4d172810
authored
Aug 19, 2019
by
Mathieu Giraud
Browse files
Merge branch 'feature-c/doc-format' into 'dev'
doc/vidjil-format.md: corrections See merge request
!507
parents
d218552b
362193f0
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#90181
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@@ -37,7 +37,9 @@ This is an almost minimal `.vidjil` file, describing clones in one sample.
The
`seg`
element is optional: clones without
`seg`
elements will be shown on the grid with '?/?'.
The
`_average_read_length`
is also optional, but allows to plot GENSCAN-like plots more precisely than getting only the length of the sequence.
All other elements are required. The
`reads.germlines`
list can have only one element the case of data on a unique locus.
There is here one clone on the
`TRG`
locus with a designation
`TRGV5*01 5/CC/0 TRGJ1*02`
.
There is here one clone on the
`TRG`
locus with a designation (
`name`
)
`TRGV5*01 5/CC/0 TRGJ1*02`
.
Note that this
`name`
is just used to name the clone.
The actual values used for X- and Y- axis in the V/J grid plot are
`seg.5.name`
and
`seg.3.name`
fields.
Note that other elements could be added by some program (such as
`tag`
, to identify some clones,
or
`clusters`
, to further cluster some clones, see below).
...
...
@@ -65,6 +67,7 @@ or `clusters`, to further cluster some clones, see below).
"
clones
"
:
[
{
"
id
"
:
"
clone-001
"
,
"
name
"
:
"
TRGV5*01 5/CC/0 TRGJ1*02
"
,
"
sequence
"
:
"
CTCATACACCCAGGAGGTGGAGCTGGATATTGATACTACGAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGCCTTATTATAAGAAACTCTTTGGCAGTGGAAC
"
,
"
reads
"
:
[
243241
],
"
_average_read_length
"
:
[
119.3
],
...
...
@@ -85,7 +88,7 @@ or `clusters`, to further cluster some clones, see below).
## `.vidjil` file – several related samples
This a
`.vidjil`
file obtained by merging with
`fuse.py`
two
`.vidjil`
files corresponding to two samples.
Clones that have a same
`id`
are gathered (see 'What is a clone?', above).
Clones that
are from different files but that
have a same
`id`
are gathered (see 'What is a clone?', above).
It is the responsibility of the program generating the initial
`.vidjil`
files to choose these
`id`
to
do a correct gathering.
...
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