.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH TRADIS_GENE_INSERT_SITES "1" "March 2017" "tradis_gene_insert_sites 1.3.1" "User Commands"
.SH NAME
tradis_gene_insert_sites \- bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file
.SH SYNOPSIS
.B tradis_gene_insert_sites

.SH DESCRIPTION
Take in a plot file(s) and an embl file and produce a tab delimited file with insert site details to use as input to an R script to t
est for essentiality.
.TP
\fB\-o\fR|output_suffix
<suffix to add to output files (optional, default = tradis_gene_insert_sites.csv)>
.TP
\fB\-trim5\fR
<trim insertion sites from 5' end of gene (optional, default = 0)>
.TP
\fB\-trim3\fR
<trim insertion sites from 3' end of gene (optional, default = 0)>
.TP
\fB\-j\fR|joined_output
<output a single file with all info. default = one file per input file>
.TP
\fB\-h\fR|help
display this message
.SH EXAMPLES
.IP
tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz
.IP
tradis_gene_insert_sites my_annotation.embl my_insert_site_plot
.TP
# multiple plot files
tradis_gene_insert_sites my_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz
.TP
# specify an output suffix this will result in a file named my_insert_site_plot1.my_output.csv
tradis_gene_insert_sites \fB\-o\fR my_output.csv my_annotation.embl my_insert_site_plot1
.TP
# Trim insertion sites from start or end of gene
tradis_gene_insert_sites my_annotation.embl \fB\-trim5\fR 0.1 \fB\-trim3\fR 0.1 my_annotation.embl my_insert_site_plot.gz
.PP
The trim parameter is the fraction of the gene length trimmed.
.TP
# place all info into a single file
tradis_gene_insert_sites \fB\-o\fR output_suffix.csv \fB\-j\fR my_annotation.embl plot1.gz plot2.gz plot3.gz
.PP
Resulting file: joined_output.output_suffix.csv
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.