Commit d79faf17 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/user.md: details, typos

parent 8d77af1c
......@@ -77,26 +77,25 @@ to learn the essential features of Vidjil.
## The info panel (upper left panel)
- patient/run/set information
user can put some informations in this case to retain about the set of samples
- locus
germline used for analyzing the data. In case of multi-locus
- *patient/run/set information.*
- *locus.* Germline(s) used for analyzing the data. In case of multi-locus
data, you can select what locus should be displayed (see [locus.html](./locus.html))
- analysis
name (without extension) of the loaded file used for displaying the data
- sample
name of the current sample. You can also change the current sample by clicking directly on his name in the graph panel (when available).
\#The name can be edited (“edit”).
- date
indicate the date of the run of the current sample (edit with the database, on the patient/run/sample set tab).
You can change the sample viewed by clicking on the `←` and `→` buttons. A cycling view is available by the fix button.
- analyzed reads
number of reads where the underlying RepSeq algorithm found a V(D)J recombination, for that sample
- *analysis.* Name (without extension) of the loaded file.
- *sample.* Name of the current sample.
<!-- The name can be edited (“edit”). -->
- *date.* Date of the current sample
(can be edited in the database, on the patient/run/sample set tab).
When displaying multiple samples from a same patient/run/set,
you can change the sample viewed by clicking on the `←` and `→` buttons,
or cycle trough them by clicking on the "▶" button.
- *analyzed reads.* umber of reads where the underlying RepSeq algorithm
found a V(D)J recombination, for that sample.
See *Number of analyzed reads* below.
- total
total number of reads for that sample
By hovering the mouse, one also sees the *total*
number of reads for that sample.
## The list of clones (left panel)
......@@ -118,8 +117,6 @@ then followed by the J gene `TRGJ1*02`, with `6` nucleotides deleted at its star
according to this clone. You must specify the expected concentration in the
“expected size” field (e.g. 0.01 for 1%). See *Control with standard/spike* below.
- The “i” button displays additional information on each clone.
- The list can be sorted on V genes, J genes or clone abundance.
The “+” and “-” allow respectively to un-cluster or re-cluster all clones that have
already been clustered.
......@@ -135,7 +132,7 @@ then followed by the J gene `TRGJ1*02`, with `6` nucleotides deleted at its star
displayed.
### Detailed information on each clone
The "i" button opens a window showing detailed information (V(D)J designation,
The “🛈” button opens a window showing detailed information (V(D)J designation,
e-value, number of reads) about each clone.
In addition, depending on what the user launched on this clone, we may also
......@@ -224,7 +221,7 @@ They are just different ways to group samples.
Sets can for example gather a set of samples of a same experiment.
Runs can be used to gather samples that have been sequenced in the same run.
## Permanent address (URLs) to a set of samples
## Permanent address (URL) to a set of samples
Addresses such as <http://app.vidjil.org/?set=3241&config=39> directly target a set of samples (here the public dataset L3), possibly with your saved analysis.
Moreover, the address also encodes other parameters, for instance <http://app.vidjil.org/?set=3241&config=39&plot=v,size,bar&clone=11,31> (selected axes and selected clones).
......@@ -246,7 +243,7 @@ which is not the case for the results (unless the user wants so).
You can see which samples have been processed with the selected
config, and access to the results (`See results`, bottom right).
Adding a sample
### Adding a sample
To add a sample (`+ sample`), you must add at least one sample file. Each sample file must
be linked to a patient, a run or a set. One of those fields will be automatically
......@@ -256,7 +253,7 @@ patient, run or sets. It is advised to fill in both fields (when it makes
sense). However please note that the correspondig patients, runs and sets must have
been created beforehand.
Pre-processing
### Pre-processing
The sample files may be preprocessed, by selecting a *pre-process scenario* when adding a sample.
At the moment the only preprocess avalaible on the public server (<http://app.vidjil.org>) are the paired-end read merging.
......@@ -282,7 +279,7 @@ 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 human configurations with vidjil-algo are « TRG », « IGH », « multi » (`-g germline`), « multi+inc » (`-g germline -i`), « multi+inc+xxx » (`-g germline -i -2`, default advised configuration).
The base human configurations with **vidjil-algo** are « TRG », « IGH », « multi » (`-g germline`), « multi+inc » (`-g germline -i`), « multi+inc+xxx » (`-g germline -i -2`, default advised configuration).
See [locus.html](./locus.html) for information on these configurations.
There are also configuration for other species and for other RepSeq algorithms, such as « MiXCR ».
The server mainteners can add new configurations tailored to specific needs, contact us if you have other needs.
......@@ -313,7 +310,7 @@ another organisation.
The different permissions that can be attributed are:
- Read: Permissions to sview patients/runs/sets to which a group or organisation has access to
- Read: Permissions to view patients/runs/sets to which a group or organisation has access to
- Create: Permissions to create patients/runs/sets
- Upload: Permissions to upload samples to the patients/runs/sets of a group
- Run: Permissions to run vidjil on an uploaded samples to the patients/runs/sets of a group
......@@ -511,7 +508,7 @@ There can be several causes leading to bad ratios:
## Clone coverage
In vidjil-algo,
In **vidjil-algo**,
the clone coverage is the ratio of the length of the clone consensus sequence
to the median read length in the clone.
A consensus sequence is
......
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