Commit 053b52b5 authored by Mikaël Salson's avatar Mikaël Salson
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Merge branch 'doc/get-support' into 'dev'

doc/user.md: get help on specific sequences

See merge request !660
parents 10547fe6 92611bdc
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......@@ -9,7 +9,7 @@ pathologies, and in leukemia, are used to quantify the minimal residual
disease during patient follow-up.
With adapted [library preparation and sequencing](locus.md),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html)
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
### Life scientist
......
......@@ -2,7 +2,9 @@
[V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are essential for immunological diversity.
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
High-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated [RepSeq](http://omictools.com/rep-seq-c424-p1.html) methods and software.
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
# Library preparation and sequencing for human RepSeq studies
......
......@@ -4,7 +4,9 @@ Vidjil is an open-source platform for the analysis of high-throughput sequencing
[V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are essential for immunological diversity.
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus),
high-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html) methods and software.
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
This is the help of the [Vidjil web application](http://app.vidjil.org/).
Further help can always be asked to <support@vidjil.org>. We can also arrange phone or video meeting.
......@@ -593,6 +595,24 @@ detection is.
Whenever the e-value is too large, a warning sign will be shown next to the
clone, instead of the info icon.
# How can I have further support or help on a specific sample or on some sequences?
When you have questions on specific data, we advise to use the `help > get support`
link inside the web application.
This opens a mail template with reference to the sample,
and possibly with references to the selected clones.
Indeed, the address <http://app.vidjil.org/?set=XXXXX&config=XXX&clone=XXX>
reflects the sample you are studying with a given configuration.
When you select one or several clones, the address is updated.
Note that, even knowing this address,
only the logged-in users with proper authorization can access to these data.
This includes the uploader of the data,
possibly users of the same groups if such groups were defined, and the server maintainers.
# Keyboard shortcuts
Note that some shortcuts may not work on some systems or on on some web browsers.
......
......@@ -27,7 +27,9 @@ diversity. They are also useful markers of pathologies, and in
leukemia, are used to quantify the minimal residual disease during
patient follow-up.
With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus),
high-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html) methods and software.
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
Vidjil-algo processes high-throughput sequencing data to extract V(D)J
junctions and gather them into clones. Vidjil-algo starts
......
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