Commit 62ea80f9 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/tutorial: details

Following remarks by @aurelBZH
See #2776.
parent 922ab3f3
Pipeline #10896 passed with stages
in 14 seconds
......@@ -16,7 +16,9 @@ These clones may have been computed by the Vidjil algorithm or by any other algo
\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, ``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}.
Do not open the \textit{Demo LIL-L3 (analyzed)} patient: this one contains the complete
analysis.
The Vidjil web application opens.}
This patient (patient XXX from study XXX) suffering T-ALL has one diagnosis sample,
......@@ -35,10 +37,14 @@ 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 his own way to analyze reads.
\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
Mi-Seq).}
\question{How many reads have been analyzed in the current sample?}
\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.
......@@ -49,6 +55,7 @@ For that sake you will need to display the information box by clicking on the
\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.
XXXX On détaille quelque part ? Renvoi à user.org ? Trop technique ici. XXXX
\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?}
......@@ -57,7 +64,6 @@ not been analyzed.
\subsection{Looking to a clone}
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.
......@@ -65,7 +71,7 @@ In this file (processed by the embedded algorithm), the most abundant clone
is \texttt{IGHV3-9 7/CCCGGA/17 J6*02}.
\question{Select this clone, either by clicking on the list or on the grid.
How many reads do this clone represent? (see the bottom part to the right)}
How many reads do this clone represent? (see again the bottom part to the right)}
There are several options to display the V(D)J designation.
......@@ -268,7 +274,7 @@ sequences are, and potentially you could cluster them if you'd like or tag them.
\bigskip
\textit{This part is specific to samples analyzed with the Vidjil algorithm.}
\textit{This part is specific to samples analyzed with the embedded algorithm of the Vidjil platform.}
Some clones may be less trustable than other ones\dots{} Let's see how to spot them.
\question{In the clone list, search clones with an orange warning at the
......
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