.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH TRADIS_COMPARISON "1" "March 2017" "tradis_comparison 1.3.1" "User Commands"
.SH NAME
tradis_comparison \- bio-tradis: compares two experimental conditions using the method of Dembek et al.
.SH SYNOPSIS
.B tradis_comparison
[\fI\,-h\/\fR] [\fI\,-f\/\fR] [\fI\,-t read cutoff\/\fR] [\fI\,-o outputfile.csv\/\fR] [\fI\,-p outputplot.pdf\/\fR] \fI\,--controls controls.txt --conditions conditions.txt\/\fR
.SH DESCRIPTION
Compares two experimental conditions using the method of Dembek et al.
mBio 2015. Read counts per gene are compared using edgeR. This analysis
requires experimental replicates.
.SH OPTIONS
.SS Required Arguments:
.TP
\fB\-\-controls\fR
control libraries, generally growth in a permissive condition
.TP
\fB\-\-conditions\fR
libraries exposed to the experimental condition being
compared
.SS Optional Arguments:
.TP
\fB\-o\fR
output filename
.TP
\fB\-p\fR
output filename for diagnostic plots
.TP
\fB\-f\fR
enable filtering on minimum read counts
.TP
\fB\-t\fR
if \fB\-\-filter\fR is enabled, sets minimum read count necessary in one
condition for a gene to be included in the comparison.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.