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vidjil
vidjil
Commits
8f1d824f
Commit
8f1d824f
authored
Mar 06, 2019
by
Mathieu Giraud
Browse files
doc/vidjil-algo.md: update
See
#3295
.
parent
2900822b
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doc/vidjil-algo.md
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8f1d824f
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@@ -477,11 +477,11 @@ The following options are experimental and have no consequences on the `.vdj.fa`
nor on the standard output. They instead add a
`clusters`
sections in the
`.vidjil`
file
that will be visualized in the web application.
The
`-n`
option triggers an automatic clustering using DBSCAN algorithm (Ester and al., 1996).
Using
`-n 5`
usually cluster reads within a distance of 1 mismatch (default score
The
`-
-cluster-epsilo
n`
option triggers an automatic clustering using DBSCAN algorithm (Ester and al., 1996).
Using
`-
-cluster-epsilo
n 5`
usually cluster reads within a distance of 1 mismatch (default score
being +1 for a match and -4 for a mismatch). However, more distant reads can also
be clustered when there are more than 10 reads within the distance threshold.
This behaviour can be controlled with the
`-N`
option.
This behaviour can be controlled with the
`-
cluster-
N`
option.
The
`-=`
option allows to specify a file for manually clustering two windows
considered as similar. Such a file may be automatically produced by vidjil
...
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@@ -796,10 +796,10 @@ This file will be relatively small (a few kB or MB) and can be taken again as an
## Advanced usage
```
bash
./vidjil-algo
-c
clones
-g
germline/homo-sapiens.g
-r
1
-n
5
-x
10000 demo/LIL-L4.fastq.gz
./vidjil-algo
-c
clones
-g
germline/homo-sapiens.g
-r
1
-
-cluster-epsilo
n
5
-x
10000 demo/LIL-L4.fastq.gz
# Extracts the windows with at least 1 read each (-r 1, the default being -r 5)
# on the first 10,000 reads, then cluster them into clones
# with a second clustering step at distance five (-n 5)
# with a second clustering step at distance five (-
-cluster-epsilo
n 5)
# The result of this second is in the .vidjil file ('clusters')
# and can been seen and edited in the web application.
```
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