The `--top` parameter allows to choose how many top clones per sample should
be kept. The default value is 50. Here `--top 100` means that for each sample, the top 100 clones are kept
*and followed in the other samples*, even if it is not in the top 100 of the other samples.
This allows to follow and quantify targeted clones even when there have only a few reads in some samples.
The `mrd.vidjil` file can then be fed to the web client.
## Using AIRR data
The AIRR community has published [a standard representation](http://docs.airr-community.org/en/latest/datarep/overview.html#format-specification) to describe results of immune receptor repertoire analysis.
Used by an increasing number of software, this `.tsv` format allows to easily transfer immune repertoire data between pipelines.
The [AIRR output of vidjil-algo](./vidjil-algo/#airr-tsv-output) enables to fed vidjil-algo output to other software.
Conversely, `fuse.py` is able to take one or several AIRR `.tsv` file(s) to get a `.vidjil` file that can be opened by the Vidjil web application:
@@ -30,16 +30,19 @@ recombinations and the sequences found in one or several samples.
The easiest way to get these files is to [request an account](http://app.vidjil.org/) on the public Vidjil test server.
You will then be able to upload,
manage, process your samples (`.fasta`, `.fastq`, `.gz` or `.clntab` files) directly on the web application
manage, process your samples (`.fasta`, `.fastq`, `.gz`, `.bam`, or `.clntab` files) directly on the web application
(see *The patient/experiment database and the server*), and the server behind the patient/experiment
database computes these `.vidjil` files.
Otherwise, such `.vidjil` files can be obtained:
database computes these `.vidjil` files with vidjil-algo.
Otherwise, such `.vidjil` files can be obtained either:
-from vidjil-algo (starting from
-running vidjil-algo from the command line (starting from
`.fasta`, `.fastq` or `.gz` files, see [vidjil-algo documentation](http://www.vidjil.org/doc/vidjil-algo/)).
To gather several `.vidjil` files, you have to use the [fuse.py](http://git.vidjil.org/blob/master/tools/fuse.py) script
- or by any other V(D)J analysis pipelines able to output files
respecting the `.vidjil`[file format](./format-analysis.org)(contact us if you are interested)
respecting the `.vidjil`[file format](http://www.vidjil.org/doc/vidjil-format/)
- or by using the [fuse.py](http://git.vidjil.org/blob/master/tools/fuse.py) script on the standard [AIRR representation](http://docs.airr-community.org/en/latest/datarep/overview.html#format-specification)
Contact us if you want help on converting such data.