Commit 4c1eae88 authored by Mathieu Giraud's avatar Mathieu Giraud

tuto: details

parent 77949992
......@@ -23,7 +23,7 @@ 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
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\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\,\%)'}}
......@@ -32,7 +31,7 @@ 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/\#reads-without-detected-recombinations}{vidjil.org/doc/vidjil-algo\#reads-without-detected-recombinations}}
\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
......
\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{ 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
......
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