Commit 08a1a6cc authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'doc/update-tutorial' into dev

parents f622397e 4884742e
Pipeline #69393 passed with stages
in 5 minutes and 25 seconds
......@@ -9,7 +9,7 @@
\usepackage{hyperref}
\newlength\myleftmargin
\setlength{\myleftmargin}{2cm}
\usepackage[margin=3.2cm, top=2cm, bottom=2cm,left=\myleftmargin,a4paper]{geometry}
\usepackage[margin=3.5cm, top=2cm, bottom=2cm,left=\myleftmargin,a4paper]{geometry}
\usepackage{graphicx}
\usepackage{caption}
\usepackage{array}
......@@ -46,7 +46,7 @@
\end{minipage}
\hfill
\begin{minipage}[c]{.2\textwidth}
\includegraphics[width=\textwidth]{grid-0}
%\includegraphics[width=\textwidth]{grid-0}
\end{minipage}
}
\makeatother
\documentclass[10pt]{article}
\documentclass[11pt]{article}
\usepackage[english]{babel}
\input{common-headers}
\title{Mastering the Vidjil web application:\\ Browsing and analysing clones
\title{Mastering the Vidjil web application \\[1ex] Day 1 -- Browsing and analysing clones
}
\widowpenalty10000
\clubpenalty10000
\begin{document}
\maketitle
......@@ -18,6 +21,12 @@ or by any other algorithm.}
\bigskip
\centerline{\includegraphics[width=.8\textwidth]{../../../vdj/vdj/doc/com/screenshots/vidjil-11-TRG-combined.png}}
\bigskip
\question{Connect to the public server (\url{https://app.vidjil.org}), either with your account
or the demo account (\texttt{demo@vidjil.org} / \texttt{demo}),
select the \textit{Demo LIL-L3 (tutorial)} patient, and click on the bottom right link, \com{see results: multi-inc-xxx}.
......@@ -38,35 +47,9 @@ In the following sections, we focus on the diagnosis sample.
% how to view and filter clones and
The section~\ref{sec:tracking} will deal with the comparison of several samples.
\section{Assessing the quality of the run and of the analysis}
The Vidjil web application allows to run several ``RepSeq'' (immune repertoire analysis) algorithms.
Each RepSeq algorithm has its own definition of what a clone is (or, more precisely
a clonotype), how to output its sequence and how to assign a V(D)J designation.
The number of analyzed reads will depend on the algorithm used.
This sample has been processed using the Vidjil algorithm.
\marginpar{The percentage of analyzed reads can range from .01\,\% (for
RNA-Seq or capture data) to 98-99\,\% (for very high-quality runs mostly on
Illumina).}
\question{How many reads have been analyzed in the current sample with the embedded algorithm ?}
Now we will try to assess the reason why some reads were not analyzed in our
sample.
This might reflect a problem during the sequencing protocol\dots or that could
be normal.
For that sake you will need to display the information box by clicking on the
\textit{i} in the upper left part.
\question{What are the average read lengths on IGH? and on TRG?}
The lines starting with \texttt{UNSEG} display the reasons why some reads have
not been analyzed.
You can see what those reasons mean in the online documentation of the
algorithm: \href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{vidjil.org/doc/vidjil-algo\#unsegmentation-causes
}
\question{What are the major causes explaining the reads have not been
analyzed? Also have a look at the average read lengths of these causes. Do
you notice something regarding the average read lengths?}
\input{tutorial-quality}
\input{tutorial-clones}
......@@ -76,13 +59,14 @@ algorithm: \href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{v
\centerline{\includegraphics[width=.5\textwidth]{./grid-1}}
\end{document}
\newpage
\input{tutorial-server}
\input{tutorial-several-samples}
\input{tutorial-export}
\input{tutorial-server}
\vfill
\flushright \it Aurélien Béliard, Aurélie Caillault, Mathieu Giraud, Tatiana Rocher, Mikaël Salson, Florian Thonier
......
......@@ -23,8 +23,11 @@ The lines starting with \texttt{UNSEG} display the reasons why some reads have
not been analyzed.
You can see what those reasons mean in the online documentation of the
algorithm: \href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{vidjil.org/doc/vidjil-algo\#unsegmentation-causes
}
algorithm:
\centerline{\href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{vidjil.org/doc/vidjil-algo\#unsegmentation-causes
}}
\question{What are the major causes explaining the reads have not been
analyzed? Also have a look at the average read lengths of these causes. Do
you notice something regarding the average read lengths?}
......
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