Commit 4071b260 authored by mcariou's avatar mcariou
Browse files

clean space

parent 8e6a495a
\documentclass[11pt, oneside]{article} % use "amsart" instead of "article" for AMSLaTeX format
%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
%\geometry{letterpaper} % ... or a4paper or a5paper or ...
%\geometry{landscape} % Activate for for rotated page geometry
%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
% TeX will automatically convert eps --> pdf in pdflatex
%\usepackage{amssymb}
\usepackage[utf8]{inputenc}
%\usepackage[cyr]{aeguill}
%\usepackage[francais]{babel}
%\usepackage{hyperref}
\usepackage{graphicx}
\usepackage{titling}
\usepackage{listings}
\usepackage{upquote}
\usepackage{hyperref}
\usepackage{xcolor}
%\definecolor{gray}{rgb}{0.5,0.5,0.5}
\lstnewenvironment{code}[1][]{
\lstset{
% upquote=true,
columns=flexible,
basicstyle=\ttfamily,
language=[LaTeX]TeX,
texcsstyle=*\color{blue},
commentstyle=\color{gray},
frame=single,
rulecolor=\color{green!5},
backgroundcolor=\color{green!5},
}
}{}
\title{Reference phylogeny for Legionella}
\author{Marie Cariou}
\date{Septembre 2021} % Activate to display a given date or no date
\begin{document}
\maketitle
\tableofcontents
\newpage
\section{Introduction}
\subsection{Objective}
We aim at the reconstruction of a reference phylogeny for all legionella species (contained in Bustein et al. 2016 or Gupta et al. 2020) and 5 selected strains of \textit{legionella pneumophila}
We chose to use the 78 genes selected by Burstein et al. 2016. The first objective is then to recover individual gene sequences for all these genomes.
\subsection{Data}
Data from the first publication:
\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050043/}
\url{https://www.ncbi.nlm.nih.gov/bioproject/PRJNA285910}
<<>>=
home<-"~/Documents/CIRI_BIBS_projects/2021_04_Doublet/pipeline/phylolegio/"
data<-paste0(home, "data/")
datalist1<-list.files(data, pattern="NIHMS817051")
datalist1
@
<<>>=
tab1<-read.table(paste0(data, datalist1[1]), skip=2, sep="\t", fill=TRUE, header=TRUE, comment.char = "")
head(tab1)
@
<<>>=
tabPRJNA<-read.table(paste0(data, "PRJNA285910_AssemblyDetails.txt"), header=FALSE, sep="\t", skip=2, fill=TRUE)
tabPRJNA<-tabPRJNA[,1:6]
names(tabPRJNA)<-c("Assembly", "Level", "WGS", "BioSample", "Strain", "Taxonomy")
@
\url{https://pubmed.ncbi.nlm.nih.gov/33881638/}
<<>>=
datalist2<-list.files(data, pattern="Gupta")
datalist2
gupta1<-read.table(paste0(data, datalist2[1]), sep="\t", fill=TRUE, header=TRUE, comment.char = "")
head(gupta1)
gupta2<-read.table(paste0(data, datalist2[2]), sep="\t", fill=TRUE, header=TRUE, comment.char = "")
head(gupta2)
head(tab1)
@
Je ne parviens pas à retrouver la correspondance entre les numéro d'accession fourni dans le tableau 1 de la publi et des numéros d'accession d'assemblage GEnBank
<<>>=
ncbi<-read.table(paste0(data, "tab_ncbi_file.csv"), sep=";", fill=TRUE, header=TRUE, comment.char = "")
sp<-c("adelaidensis", "birminghamensis", "brunensis", "cherrii")
ncbi2<-read.table(paste0(data, "tab_ncbi_contigs_parsed.csv"), sep=";", fill=TRUE, header=TRUE, comment.char = "")
@
\section{Get genes sequences}
\subsection{Get sequences from Burstein et al.}
\subsection{Get 78 sequences from Gupta species}
\subsection{Get legionella pneumophila strains sequences}
\section{Phylogeny}
\subsection{Genes alignement}
\subsection{Concatenate}
\subsection{Supertree}
\end{document}
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment