Commit c4df4ea4 authored by Mathieu Giraud's avatar Mathieu Giraud

tuto: \reponse

parent ee316680
...@@ -30,6 +30,9 @@ ...@@ -30,6 +30,9 @@
\setlength{\marginparsep}{1em} \setlength{\marginparsep}{1em}
\setlength{\marginparwidth}{3cm} \setlength{\marginparwidth}{3cm}
\newcommand\reponse[1]{\textcolor{white}{#1}}
\newcommand\fl{\,\ensuremath{\longrightarrow}\,}
\let\oldmarginpar\marginpar \let\oldmarginpar\marginpar
\renewcommand\marginpar[1]{\oldmarginpar{\footnotesize\itshape #1}} \renewcommand\marginpar[1]{\oldmarginpar{\footnotesize\itshape #1}}
......
...@@ -12,7 +12,7 @@ is \texttt{IGHV3-9 7/CCCGGA/17 J6*02}. ...@@ -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. \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)} 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. There are several options to display the V(D)J designation.
...@@ -35,8 +35,8 @@ slider to its right end. ...@@ -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 \question{Notice how the IGH smaller clones percentage (second clone displayed in the list) changes. What was its
initial value? What is it now?} initial value? What is it now?}
\textcolor{white}{ filter set to 50 -> IGH smaller clones 10.11\,\%\\* \reponse{filter set to 50 \fl IGH smaller clones 10.11\,\%\\*
filter set to 100 -> IGH smaller clones 8.92\,\%\\*} filter set to 100 \fl IGH smaller clones 8.92\,\%\\*}
The \textit{smaller clones} correspond to clones that are not displayed The \textit{smaller clones} correspond to clones that are not displayed
because they are never among the most abundant ones. because they are never among the most abundant ones.
......
...@@ -12,7 +12,7 @@ This sample has been processed using the Vidjil algorithm. ...@@ -12,7 +12,7 @@ This sample has been processed using the Vidjil algorithm.
Illumina).} Illumina).}
\question{How many reads have been analyzed in the current sample with the embedded algorithm ?} \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 Now we will try to assess the reason why some reads were not analyzed in our
sample. sample.
...@@ -22,9 +22,9 @@ For that sake you will need to display the information box by clicking on the ...@@ -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. \textit{i} in the upper left part.
\question{What are the average read lengths on IGH? and on TRG?} \question{What are the average read lengths on IGH? and on TRG?}
\textcolor{white}{ In the Analysis log row under "av.len"\\* \reponse{In the Analysis log row, under \com{av. len}\\*
IGH -> 314.5\\* IGH \fl 314.5\\*
TRG -> 197.6 } TRG \fl 197.6 }
The lines starting with \texttt{UNSEG} display the reasons why some reads have The lines starting with \texttt{UNSEG} display the reasons why some reads have
not been analyzed. not been analyzed.
...@@ -39,5 +39,5 @@ algorithm: ...@@ -39,5 +39,5 @@ algorithm:
you notice something regarding the average read lengths?} 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.\\* \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. } 2. The may be too short to cover enough of the V or J genes to be detected. }
\ No newline at end of file
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