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.\"
.IX Title "Bio::Tradis::RunTradis 3pm"
.TH Bio::Tradis::RunTradis 3pm "2020-01-11" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tradis::RunTradis \- Perform all steps required for a tradis analysis
.SH "VERSION"
.IX Header "VERSION"
version 1.4.5
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Takes a fastq file with tags already attached, filters the tags matching user input,
removes the tags, maps to a reference (.fa) and generates insertion site plots for use in
Artemis (or other genome browsers), mapped \s-1BAM\s0 files for each lane and a statistical summary of the analysis.
.PP
.Vb 1
\&   use Bio::Tradis::RunTradis;
\&   
\&   my $pipeline = Bio::Tradis::RunTradis\->new(
\&                                        fastqfile => \*(Aqabc\*(Aq,  
\&                                        reference => \*(Aqabc\*(Aq,
\&                                        tag => \*(Aqabc\*(Aq,
\&                                        tagdirection => \*(Aq5\*(Aq|\*(Aq3\*(Aq
\&   );
\&   $pipeline\->run_tradis();
.Ve
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.SS "Required"
.IX Subsection "Required"
.IP "\(bu" 4
\&\f(CW\*(C`fastqfile\*(C'\fR \- file containing a list of fastqs (gzipped or raw) to run the 
			complete analysis on. This includes all (including 
			intermediary format conversion and sorting) steps starting from
			filtering.
.IP "\(bu" 4
\&\f(CW\*(C`reference\*(C'\fR \- path to/name of reference genome in fasta format (.fa)
.SS "Optional"
.IX Subsection "Optional"
.IP "\(bu" 4
\&\f(CW\*(C`mismatch\*(C'\fR \- number of mismatches to allow when filtering/removing the tag. Default = 0
.IP "\(bu" 4
\&\f(CW\*(C`tagdirection\*(C'\fR \- direction of the tag, 5' or 3'. Default = 3
.IP "\(bu" 4
\&\f(CW\*(C`mapping_score\*(C'\fR \- cutoff value for mapping score when creating insertion site plots. Default = 30
.IP "\(bu" 4
\&\f(CW\*(C`tag\*(C'\fR \- TraDIS tag to filter and then remove
.SH "METHODS"
.IX Header "METHODS"
\&\f(CW\*(C`run_tradis\*(C'\fR \- run complete analysis with given parameters
.SH "AUTHOR"
.IX Header "AUTHOR"
Carla Cummins <path\-help@sanger.ac.uk>
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
.PP
This is free software, licensed under:
.PP
.Vb 1
\&  The GNU General Public License, Version 3, June 2007
.Ve