Commit c2af6d25 authored by Laros's avatar Laros
Browse files

Added coverage slides.

parent f9d107d5
../../submodules/presentation/Makefile
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../../submodules/presentation/beamerthemelumc.sty
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% Alter these four lines for a new presentation.
\providecommand{\me}{Jeroen F. J. Laros}
\providecommand{\myTitle}{Copy Number of Substrings}
\providecommand{\myConference}{Work discussion}
\providecommand{\myDate}{Tuesday, 13 October 2009}
% Now go to %%% BEGIN PRESENTATION %%%
\documentclass[a4, portrait]{seminar}
\usepackage{semcolor} % For coloured text.
\usepackage{slidesec} % For section headings.
\usepackage{newcent} % This is a better font for presentations.
\input{seminar.bug}
\usepackage{graphicx} % For pictures.
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{\bf
\small{\me}\\
\small{Department of Human Genetics}\\
\small{Center for Human and Clinical Genetics}
}
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\end{center}
\vfill
\end{slide}
\slideframe{PRES} % Use the body template.
%%% BEGIN PRESENTATION %%%
\begin{slide}
\slideheading{Problem description}
A sequenced string is usually mapped back to a reference genome.
Ideally, the sequenced string is \emph{unique}, in this case the mapping can
be done in only one way.
Unfortunately, when using a fixed length read length, the chance that a read
is not unique increases when the length decreases.
\begin{itemize}
\item Map everything on the first occurrence.
\item Map everything randomly on one of the occurrences.
\end{itemize}
\vfill
\end{slide}
\begin{slide}
\slideheading{Taking notice of the problem}
By analysing the reference genome itself, we can predict how many times each
read occurs.
We do that by ``counting'' each substring of a certain length.
The output is an array, indexed by the substring itself, which contains the
count number.
\begin{itemize}
\item Detect insertions or deletions by a variance of these counts.
\item
\item Verification in general.
\end{itemize}
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\vfill
\end{slide}
\begin{slide}
\slideheading{Practical solution}
Preliminary research [Rietveld 2009] showed that indexing the entire human
genome can be done efficiently (half an hour). With non-dedicated hardware
and low memory capabilities about eight hours.
Output consists of a truncated-suffix array (suffixes truncated at any length),
this array can be used to determine all occurrences of...
\vfill
\end{slide}
\begin{slide}
\rput(11.4,0.6){\includegraphics[scale=0.1]{Gen2Phen}}
\slideheading{Questions?}
\vfill
\label{LastPage}
\end{slide}
\end{document}
../../submodules/presentation/gen2phen_logo.eps
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../../submodules/presentation/lgtc_logo.eps
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../../submodules/presentation/lumc_logo.eps
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../../submodules/presentation/lumc_logo_small.eps
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../../submodules/presentation/nbic_logo.eps
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../../submodules/presentation/ngi_logo.eps
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../../submodules/presentation/nwo_logo_en.eps
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../../submodules/presentation/nwo_logo_nl.eps
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../../submodules/presentation/ul_logo.eps
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