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 @@ ...@@ -9,7 +9,7 @@
\usepackage{hyperref} \usepackage{hyperref}
\newlength\myleftmargin \newlength\myleftmargin
\setlength{\myleftmargin}{2cm} \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{graphicx}
\usepackage{caption} \usepackage{caption}
\usepackage{array} \usepackage{array}
...@@ -46,7 +46,7 @@ ...@@ -46,7 +46,7 @@
\end{minipage} \end{minipage}
\hfill \hfill
\begin{minipage}[c]{.2\textwidth} \begin{minipage}[c]{.2\textwidth}
\includegraphics[width=\textwidth]{grid-0} %\includegraphics[width=\textwidth]{grid-0}
\end{minipage} \end{minipage}
} }
\makeatother \makeatother
\documentclass[10pt]{article} \documentclass[11pt]{article}
\usepackage[english]{babel} \usepackage[english]{babel}
\input{common-headers} \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} \begin{document}
\maketitle \maketitle
...@@ -18,6 +21,12 @@ or by any other algorithm.} ...@@ -18,6 +21,12 @@ or by any other algorithm.}
\bigskip \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 \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}), 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}. 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. ...@@ -38,35 +47,9 @@ In the following sections, we focus on the diagnosis sample.
% how to view and filter clones and % how to view and filter clones and
The section~\ref{sec:tracking} will deal with the comparison of several samples. 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. \input{tutorial-quality}
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-clones} \input{tutorial-clones}
...@@ -76,13 +59,14 @@ algorithm: \href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{v ...@@ -76,13 +59,14 @@ algorithm: \href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{v
\centerline{\includegraphics[width=.5\textwidth]{./grid-1}} \centerline{\includegraphics[width=.5\textwidth]{./grid-1}}
\end{document}
\newpage \newpage
\input{tutorial-server}
\input{tutorial-several-samples} \input{tutorial-several-samples}
\input{tutorial-export} \input{tutorial-export}
\input{tutorial-server}
\vfill \vfill
\flushright \it Aurélien Béliard, Aurélie Caillault, Mathieu Giraud, Tatiana Rocher, Mikaël Salson, Florian Thonier \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 ...@@ -23,8 +23,11 @@ The lines starting with \texttt{UNSEG} display the reasons why some reads have
not been analyzed. not been analyzed.
You can see what those reasons mean in the online documentation of the 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 \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 analyzed? Also have a look at the average read lengths of these causes. Do
you notice something regarding the average read lengths?} you notice something regarding the average read lengths?}
......
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