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% Document Info
\author{rekins}
\pdfinfo{
  /Title (experimental-design.pdf)
  /Creator (Cheatography)
  /Author (rekins)
  /Subject (Experimental design Cheat Sheet)
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\noindent
\begin{multicols}{3}
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    {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent
        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
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\begin{tabulary}{11cm}{L}
    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{Experimental design Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{rekins} via \textcolor{DarkBackground}{\uline{cheatography.com/26597/cs/7480/}}}
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\noindent
\begin{multicols}{3}
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  \SetRowColor{FootBackground}
  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}rekins \\
  \uline{cheatography.com/rekins} \\
  \end{tabulary}
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  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Published 31st August, 2020.\\
   Updated 9th June, 2016.\\
   Page {\thepage} of \pageref{LastPage}.
\end{tabulary}
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  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Sponsor}}  \\
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  \vspace{-5pt}
  %\includegraphics[width=48px,height=48px]{dave.jpeg}
  Measure your website readability!\\
  www.readability-score.com
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\begin{document}
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\begin{multicols*}{3}

\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{NGS Coverage}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{5.377cm}}{{\bf{Coverage = Total raw output /  Target sequencing size}}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{50x for de novo sequencing} \tn 
% Row Count 3 (+ 1)
% Row 2
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\mymulticolumn{1}{x{5.377cm}}{30x coverage for resequencing and transcriptomics} \tn 
% Row Count 4 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.24425 cm} x{3.73275 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Target sequencing size estimation}}  \tn
% Row 0
\SetRowColor{LightBackground}
GENOME & Number of samples x target genome size \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
AMPLICON & Number of molecules x average molecule size \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
\seqsplit{TRANSCRIPTOME} & N genes x average length (bp) \tn 
% Row Count 6 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.51041 cm} x{1.3731 cm} x{1.69349 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{3}{x{5.377cm}}{\bf\textcolor{white}{Genome Information}}  \tn
% Row 0
\SetRowColor{LightBackground}
{\bf{Species}} & \{\{ar\}\}{\bf{Size}} & \{\{ar\}\}{\bf{N genes}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
{\emph{E. coli}} & \{\{ar\}\}5 Mbp & \{\{ar\}\}4600 \tn 
% Row Count 3 (+ 1)
% Row 2
\SetRowColor{LightBackground}
{\emph{S. cerevisiae}} & \{\{ar\}\}13 Mbp & \{\{ar\}\}6000 \tn 
% Row Count 5 (+ 2)
% Row 3
\SetRowColor{white}
{\emph{A. thaliana}} & \{\{ar\}\}130 Mbp & \{\{ar\}\}27000 \tn 
% Row Count 7 (+ 2)
% Row 4
\SetRowColor{LightBackground}
{\emph{H. sapiens}} & \{\{ar\}\}3 Gbp & \{\{ar\}\}25000 \tn 
% Row Count 8 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}---}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.37841 cm} x{0.8354 cm} x{0.8354 cm} x{1.12779 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{4}{x{5.377cm}}{\bf\textcolor{white}{Variation Analysis}}  \tn
% Row 0
\SetRowColor{LightBackground}
{\bf{Technology}} & \{\{ac\}\}{\bf{WGS}} & \{\{ac\}\}{\bf{WES}} & \{\{ac\}\}{\bf{RNA-seq}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Mut, Indels & \{\{ac\}\}Y & \{\{ac\}\}coding & \{\{ac\}\}\textasciitilde{}coding \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
CNV & \{\{ac\}\}Y & \{\{ac\}\}coding & \{\{ac\}\}N \tn 
% Row Count 6 (+ 2)
% Row 3
\SetRowColor{white}
Subclonal & \{\{ac\}\}N & \{\{ac\}\}Y & \{\{ac\}\}N \tn 
% Row Count 7 (+ 1)
% Row 4
\SetRowColor{LightBackground}
Fusions & \{\{ac\}\}\textasciitilde{}Y & \{\{ac\}\}N & \{\{ac\}\}Y \tn 
% Row Count 8 (+ 1)
% Row 5
\SetRowColor{white}
Expression (variants) & \{\{ac\}\}N & \{\{ac\}\}N & \{\{ac\}\}Y \tn 
% Row Count 10 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}----}
\SetRowColor{LightBackground}
\mymulticolumn{4}{x{5.377cm}}{{\bf{{\emph{Filters for somatic variants detection:}} Paired normal tissue, Minor Allele Frequency (MAF) \textgreater{}0.1\% in dbSNP, 1000 genomes, Database of Genomic Variant (DGV).}} \newline {\bf{{\emph{WES and WGS}}: report bases not (sufficiently) covered to detect variants.}}}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}----}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{X}
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\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{INFO}}  \tn
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{{\emph{Made as support material for the break-out Genomics session - Successful Planning of Large Data Generating Experiments (Leuven, 16 March)}}% Row Count 3 (+ 3)
} \tn 
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Sequencing Depth}}  \tn
% Row 0
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\mymulticolumn{1}{x{5.377cm}}{{\bf{D = Total raw output / read size}}} \tn 
% Row Count 1 (+ 1)
% Row 1
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\mymulticolumn{1}{x{5.377cm}}{Related to coverage, the sequencing depth computes the expected number of reads per sample.} \tn 
% Row Count 3 (+ 2)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{5.377cm}}{{\emph{For example, in human : 25,000 genes x 2,000bp x 30 coverage = 1.5Gb per sample. With a single read sequencing of 75 bp reads, this corresponds to 20 M reads per sample.}}} \tn 
% Row Count 7 (+ 4)
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.41887 cm} x{1.32733 cm} x{1.8308 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{3}{x{5.377cm}}{\bf\textcolor{white}{Required Sequencing Depth (D)}}  \tn
% Row 0
\SetRowColor{LightBackground}
{\bf{RNA quality}} & \{\{ac\}\}{\bf{mRNA}} & \{\{ac\}\}{\bf{total RNA}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Good & \{\{ac\}\}D & \{\{ac\}\}2D \tn 
% Row Count 3 (+ 1)
% Row 2
\SetRowColor{LightBackground}
Degraded & \{\{ac\}\}2D & \{\{ac\}\}4D \tn 
% Row Count 4 (+ 1)
% Row 3
\SetRowColor{white}
Bad & \{\{ac\}\}4D & \{\{ac\}\}8D \tn 
% Row Count 5 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}---}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.04425 cm} x{1.37841 cm} x{1.04425 cm} p{0.71009 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{4}{x{5.377cm}}{\bf\textcolor{white}{Specifications (Illumina)}}  \tn
% Row 0
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{\bf{Platform}} & {\bf{Max read length}} & {\bf{Max N reads}} & {\bf{Output}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
MiSeq & 2x300 bp & 25 M & 15 Gb \tn 
% Row Count 3 (+ 1)
% Row 2
\SetRowColor{LightBackground}
NextSeq Medium & 2x150 bp & 130 M & 39 Gb \tn 
% Row Count 5 (+ 2)
% Row 3
\SetRowColor{white}
NextSeq High & 2x150 bp & 400 M & 120 Gb \tn 
% Row Count 7 (+ 2)
% Row 4
\SetRowColor{LightBackground}
HiSeq2500 Rapid & 2x250 bp & 600 M & 300 Gb \tn 
% Row Count 9 (+ 2)
% Row 5
\SetRowColor{white}
HiSeq3000 & 2x150 bp & 2500 M & 750 Gb \tn 
% Row Count 10 (+ 1)
% Row 6
\SetRowColor{LightBackground}
HiSeq2500 High & 2x125 bp & 4000 M & 1 Tb \tn 
% Row Count 12 (+ 2)
% Row 7
\SetRowColor{white}
HiSeq4000 & 2x150 bp & 5000 M & 1.5 Tb \tn 
% Row Count 13 (+ 1)
% Row 8
\SetRowColor{LightBackground}
HiSeq X Ten & 2x150 bp & 6000 M & 1.8 Tb \tn 
% Row Count 15 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}----}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{0.87717 cm} x{1.42018 cm} x{1.12779 cm} p{0.75186 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{4}{x{5.377cm}}{\bf\textcolor{white}{Number of samples per application}}  \tn
% Row 0
\SetRowColor{LightBackground}
{\bf{Platform}} & {\bf{TotalRNA (40M reads)}} & {\bf{WES (\textgreater{}90\% \textgreater{}10x)}} & {\bf{WGS (30x)}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
MiSeq & NA & NA & NA \tn 
% Row Count 3 (+ 1)
% Row 2
\SetRowColor{LightBackground}
NextSeq Medium & 3 & 3 & NA \tn 
% Row Count 5 (+ 2)
% Row 3
\SetRowColor{white}
NextSeq High & 10 & 10 & 1 \tn 
% Row Count 7 (+ 2)
% Row 4
\SetRowColor{LightBackground}
\seqsplit{HiSeq2500} Rapid & 15 & 20 & 1 \tn 
% Row Count 9 (+ 2)
% Row 5
\SetRowColor{white}
\seqsplit{HiSeq3000} & 50 & 96 & 6 \tn 
% Row Count 11 (+ 2)
% Row 6
\SetRowColor{LightBackground}
\seqsplit{HiSeq2500} High & 100 & 150 & 10 \tn 
% Row Count 13 (+ 2)
% Row 7
\SetRowColor{white}
\seqsplit{HiSeq4000} & 125 & 180 & 12 \tn 
% Row Count 15 (+ 2)
% Row 8
\SetRowColor{LightBackground}
HiSeq X Ten & NA & NA & 16 \tn 
% Row Count 17 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}----}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{0.84609 cm} x{4.13091 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Costs per sample (Library prep + NGS)}}  \tn
% Row 0
\SetRowColor{LightBackground}
{\bf{Cost}} & {\bf{Application}} \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
\textasciitilde{}€4000 & WGS 30x tumor, 10x germline (2x125 bp) \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
\textasciitilde{}€2500 & WES 200x tumor, 100x germline (2x125 bp) \tn 
% Row Count 6 (+ 2)
% Row 3
\SetRowColor{white}
\textasciitilde{}€750 & Total RNA seq, 20-30 M reads, stranded library, rRNA depleted (2x125 bp) \tn 
% Row Count 9 (+ 3)
% Row 4
\SetRowColor{LightBackground}
\textasciitilde{}€300 & mRNA seq, 15-20 M reads, stranded library (75 bp) \tn 
% Row Count 11 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Authors}}  \tn
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{{\bf{Rekin's Janky}}, rekins.janky@vib.be (VIB Nucleomics Core, BE) \newline % Row Count 2 (+ 2)
{\bf{Judith Boer}}, j.m.boer@erasmusmc.nl (Erasmus Medical Centre, NL) \newline % Row Count 4 (+ 2)
{\bf{Peter-Bram 't Hoen}}, P.A.C.\_t\_Hoen@lumc.nl (Leiden University Medical Center, NL) \newline % Row Count 6 (+ 2)
{\bf{Wouter Van Delm}}, wouter.vandelm@vib.be (VIB Nucleomics Core, BE)% Row Count 8 (+ 2)
} \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}


% That's all folks
\end{multicols*}

\end{document}