Commit c4df4ea4 authored by Mathieu Giraud's avatar Mathieu Giraud

tuto: \reponse

parent ee316680
......@@ -30,6 +30,9 @@
\setlength{\marginparsep}{1em}
\setlength{\marginparwidth}{3cm}
\newcommand\reponse[1]{\textcolor{white}{#1}}
\newcommand\fl{\,\ensuremath{\longrightarrow}\,}
\let\oldmarginpar\marginpar
\renewcommand\marginpar[1]{\oldmarginpar{\footnotesize\itshape #1}}
......
......@@ -12,7 +12,7 @@ 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 again the bottom part to the right)}
\textcolor{white}{ the bottom panel display information about currently selected clones -> 189 991 reads (9.665\,\%) }
\reponse{The bottom panel display information about currently selected clones \fl 189 991 reads (9.665\,\%)}
There are several options to display the V(D)J designation.
......@@ -35,8 +35,8 @@ slider to its right end.
\question{Notice how the IGH smaller clones percentage (second clone displayed in the list) changes. What was its
initial value? What is it now?}
\textcolor{white}{ filter set to 50 -> IGH smaller clones 10.11\,\%\\*
filter set to 100 -> IGH smaller clones 8.92\,\%\\*}
\reponse{filter set to 50 \fl IGH smaller clones 10.11\,\%\\*
filter set to 100 \fl IGH smaller clones 8.92\,\%\\*}
The \textit{smaller clones} correspond to clones that are not displayed
because they are never among the most abundant ones.
......
......@@ -12,7 +12,7 @@ This sample has been processed using the Vidjil algorithm.
Illumina).}
\question{How many reads have been analyzed in the current sample with the embedded algorithm ?}
\textcolor{white}{ In the upper left corner, you can see an information panel with \com{analyzed reads 1 967 338 (82.31\,\%)'}}
\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.
......@@ -22,9 +22,9 @@ 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?}
\textcolor{white}{ In the Analysis log row under "av.len"\\*
IGH -> 314.5\\*
TRG -> 197.6 }
\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.
......@@ -39,5 +39,5 @@ algorithm:
you notice something regarding the average read lengths?}
\textcolor{white}{ 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. }
\ No newline at end of file
\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. }
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