Commit ee316680 authored by Mikaël Salson's avatar Mikaël Salson
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tuto: new feature: filtering samples

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\section{Viewing and filtering clones}
\subsection{Looking to a clone}
\subsection{Looking at a clone}
Each RepSeq algorithm has its own definition of what a clone is (or, more precisely
a clonotype), and on how to output its sequence and how to assign a V(D)J designation.
......@@ -106,7 +106,24 @@ Sometimes, one wants to hide noisy or unrelated clones.
% Another way to hide clonesis to assign is to change the tag of it as ``standard (niose)`` and choose to uncheck this tag by clicking on the corresponding tile on the list of tiles at the informatons panel to switch them from a visible state to a filter one.
%%% Voir ci-dessus, déjà mis
It is also possible to filter samples that do not contain a clone. When you
have lots of samples it helps to keep the sample of interest. Here the number
of sample is quite limited, so the feature may appear less useful.
\question{\new Click on the \com{IGHV3-11 / IGHJ6} clone in the last sample, whose
abundance is around 10\,\%.
Then go in the menu at the upper-right corner of the graph (where \com{5/5}
is written) and select \com{focus on selected clones}.
By selecting this, the samples where this clone doesn't appear are hidden.
This is useful for instance to assess the contamination among dozens of
\question{You can go back to the previous view by returning into the menu and
clicking on \com{show all}. Notice also how in the menu you can select the
samples to be shown.}
\section{Analysing clone populations}
\subsection{Clustering clones through inspection of their sequences}
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