diff --git a/doc/tutorial/common-headers.tex b/doc/tutorial/common-headers.tex index 5bf21fbcd981a6bd1d1805135fe7360042b223b0..8881fed6e27d6dce89802a095f6f9662122e01b5 100644 --- a/doc/tutorial/common-headers.tex +++ b/doc/tutorial/common-headers.tex @@ -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 diff --git a/doc/tutorial/mastering-vidjil.tex b/doc/tutorial/mastering-vidjil.tex index 450368cb8992380b846e5e1709d47d5c7cfc8537..8a28f55da356d065c026f22a515f37246c80058a 100644 --- a/doc/tutorial/mastering-vidjil.tex +++ b/doc/tutorial/mastering-vidjil.tex @@ -1,10 +1,13 @@ -\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 diff --git a/doc/tutorial/tutorial-quality.tex b/doc/tutorial/tutorial-quality.tex index 6d6c377be2db1401d2ab69f77179aa519397a826..cd3d4b6696eacebdde34867e507e20bbc4949a7a 100644 --- a/doc/tutorial/tutorial-quality.tex +++ b/doc/tutorial/tutorial-quality.tex @@ -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?}