Supplemental Material for WASP: allele-specific methods for unbiased discovery of molecular quantitative trait loci

\documentclass{article} %\usepackage{scicite} \bibliographystyle{naturemag} \usepackage{times} \usepackage{graphicx} \usepackage{url} \usepackage{amsmath} \usepackage{lscape} \DeclareMathOperator{\Like}{L} \DeclareMathOperator{\logit}{logit} \DeclareMathOperator{\expit}{expit} \renewcommand\thefigure{S\arabic{figure}} \renewcommand\thetable{S\arabic{table}} \topmargin 0.0cm \oddsidemargin 0.2cm \textwidth 16cm \textheight 21cm \footskip 1.0cm \title{Supplemental Material for WASP: allele-specific software for unbiased discovery of molecular quantitative trait loci} \author{Bryce van de Geijn$^{1,2,\dagger}$, Graham McVicker$^{3,\dagger}$, Yoav Gilad$^1$, Jonathan K. Pritchard$^{3,4,5,\ast}$\\ \\ \normalsize{$^{1}$Department of Human Genetics, University of Chicago}\\ \normalsize{$^{2}$Committee on Genetics, Genomics and Systems Biology, University of Chicago}\\ \normalsize{$^{3}$Department of Genetics, Stanford University}\\ \normalsize{$^{4}$Department of Biology, Stanford University}\\ \normalsize{$^{5}$Howard Hughes Medical Institute, Stanford University}\\ \normalsize{$^\dagger$These authors contributed equally.}\\ \normalsize{$^\ast$To whom correspondence should be addressed:}\\ } \date{}

Unbiased read mapping with WASP

To detect differences in molecular phenotypes from sequencing data it is essential to remove read mapping biases, which are a major source of false positives. The WASP read mapping pipeline accomplishes this task by ensuring that the mapping of each individual read is unbiased.