Commit c679371e authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'tuto-2020' into 'dev'

Tuto 2020

Closes #2824, #2839, #2863, and #2865

See merge request !807
parents 617f475c e2b296a0
Pipeline #172338 passed with stages
in 14 minutes and 16 seconds
......@@ -9,7 +9,7 @@
\usepackage{hyperref}
\newlength\myleftmargin
\setlength{\myleftmargin}{2cm}
\usepackage[margin=3.5cm, top=2cm, bottom=2cm,left=\myleftmargin,a4paper]{geometry}
\usepackage[margin=3.5cm, top=2.5cm, bottom=2cm,left=\myleftmargin,right=5.5cm,a4paper]{geometry}
\usepackage{graphicx}
\usepackage{caption}
\usepackage{array}
......@@ -27,8 +27,14 @@
\newcommand\com[1]{\textsf{#1}}
\newcommand\question[1]{\par\noindent\textbf{\thequestionum}.~#1\addtocounter{questionum}{1}}
\setlength{\marginparsep}{1em}
\setlength{\marginparwidth}{4cm}
\newcommand\reponse[1]{\textcolor{white}{#1}}
\newcommand\fl{\,\ensuremath{\longrightarrow}\,}
\let\oldmarginpar\marginpar
\renewcommand\marginpar[1]{\oldmarginpar{\tiny#1}}
\renewcommand\marginpar[1]{\oldmarginpar{\footnotesize\itshape #1}}
\usepackage{titling}
......
......@@ -2,7 +2,8 @@
\usepackage[english]{babel}
\input{common-headers}
\title{Mastering the Vidjil web application \\[1ex] Day 1 -- Browsing and analysing clones
\title{Mastering the Vidjil web application \\[1ex] Part 1 --
Browsing and analysing clones
}
\widowpenalty10000
......@@ -22,14 +23,16 @@ or by any other algorithm.}
\bigskip
\centerline{\includegraphics[width=.8\textwidth]{../../../vdj/vdj/doc/com/screenshots/vidjil-11-TRG-combined.png}}
\centerline{\includegraphics[width=\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}.
select the \textit{Demo LIL-L3 (tutorial)} patient.
If you don't see it, search for \com{\#Demo} in the top-left search box.
Then click on the bottom right link, \com{see results: multi-inc-xxx}.
Do not open the \textit{Demo LIL-L3 (analyzed)} patient: this one contains the complete
analysis.
The Vidjil web application opens.}
......@@ -61,7 +64,7 @@ The section~\ref{sec:tracking} will deal with the comparison of several samples.
\newpage
\title{Mastering the Vidjil web application \\[1ex] Day 2 -- Dealing with
\title{Mastering the Vidjil web application \\[1ex] Part 2 -- Dealing with
samples and exporting data
}
\maketitle
......@@ -72,7 +75,7 @@ The section~\ref{sec:tracking} will deal with the comparison of several samples.
\vfill
\flushright \it Aurélien Béliard, Aurélie Caillault, Mathieu Giraud, Tatiana Rocher, Mikaël Salson, Florian Thonier
\flushright \it Aurélien Béliard, Aurélie Caillault, Marc Duez, Mathieu Giraud, Tatiana Rocher, Mikaël Salson, Florian Thonier
\\ \texttt{contact@vidjil.org}
\end{document}
This diff is collapsed.
......@@ -71,7 +71,7 @@ It can be opened by any spreadsheet software such as LibreOffice Calc or Excel f
\com{export bottom graph} button.
This exports the current view of the plot.}
\question{\new Select some clones and align them. The alignment can be
\question{ Select some clones and align them. The alignment can be
exported with the \com{export aligned fasta} button in the
\com{import/export} menu.}
\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
The Vidjil web application allows to run several ``AIRR/RepSeq'' (immune repertoire analysis) algorithms.
Each AIRR/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 ?}
\marginpar{The percentage of analyzed reads can range from .01\,\% or below (for
RNA-Seq or capture data) to 98-99\,\% or above (for amplicon libraries with high-quality runs).}
\question{How many reads have been analyzed in the current sample by Vidjil-algo?}
\reponse{In the upper left corner, you can see an information panel with \com{analyzed reads 1 967 338 (82.31\,\%)'}}
Now we will try to assess the reason why some reads were not analyzed in our
sample.
......@@ -19,16 +20,23 @@ 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?}
\reponse{In the Analysis log row, under \com{av. len}\\*
IGH \fl 314.5\\*
TRG \fl 197.6 }
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:
\centerline{\href{http://www.vidjil.org/doc/vidjil-algo\#unsegmentation-causes}{vidjil.org/doc/vidjil-algo\#unsegmentation-causes
}}
\centerline{\tt\href{http://www.vidjil.org/doc/vidjil-algo/\#reads-without-detected-recombinations}{vidjil.org/doc/vidjil-algo\#reads-without-detected-recombinations}}
\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?}
\reponse{ 1. The algorythm was not able to find a V or a J for most of the unsegmeneted reads.\\*
2. The may be too short to cover enough of the V or J genes to be detected. }
\section{Dealing with samples and patients}
We will see how to make the best use of the patient and sample database and
how to use it efficiently.
For this sake you need an account with the rights to create new patients,
For this sake you need an \textit{account} on the public server with the rights to create new patients,
runs, sets, to upload data and, preferably, to run analyses.
Therefore the demo account is not suitable.
\question{ Go to \href{https://app.vidjil.org}{\tt app.vidjil.org} and log in to your account.
You can there click on \com{request an account} if you do not currently have one.
\marginpar{The public app.vidjil.org server is for test or research use.
Do not use it for routine clinical data.
The \href{http://www.vidjil.net}{VidjilNet} consortium offers health-certified options for hosting such data.}
}
\question{ Retrieve the toy dataset at
\href{http://vidjil.org/seqs/tutorial_dataset.zip}{vidjil.org/seqs/tutorial\_dataset.zip}
\href{http://vidjil.org/seqs/tutorial_dataset.zip}{\tt vidjil.org/seqs/tutorial\_dataset.zip}
and extract the files from the archive.}
You should now have three files. We will imagine that those three files are
......@@ -15,8 +23,8 @@ a single patient. Thus we now want to upload those files and assign all of
them to a same \com{run} and each of them to a single \com{patient}.
\question{
Go to the main page of the Vidjil platform (by default
\href{https://app.vidjil.org}{app.vidjil.org}).
Go back to the main page of the Vidjil platform (by default
\href{https://app.vidjil.org}{\tt app.vidjil.org}).
You should be on the \com{patients} page.
Go at the bottom of the page and click on \com{+ new patients} to create the
three patients.
......@@ -73,6 +81,10 @@ can be suggested later on).
patient with \#B-ALL}. For patient 2, enter \texttt{\#blood sample \#CLL}.
For patient 4, enter \texttt{bone \#marrow \#B-ALL}}
\marginpar{{\bf New!}
Note that patients (and runs and samples) can also be created at once by
pasting a table from a spreadsheet editor.}
Now the three patients and the run have been created but we have not uploaded
the sequence files yet.
......
......@@ -4,7 +4,7 @@
\label{sec:tracking}
%Load now some data with several samples.
Load now some data with several samples, such as again the \textit{Demo LIL-L3} dataset.
The \textit{time graph} shows the evolution of the top clones of each sample into all the samples.
Bear in mind that to ensure readability at most 50 curves are displayed in this graph.
\marginpar{When loading data with only one sample, the time graph is replaced by a second bar/grid plot.}
......
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