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.\"
.IX Title "Bio::Tradis::RemoveTags 3pm"
.TH Bio::Tradis::RemoveTags 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::RemoveTags \- Remove tags from seqs a fastq file
.SH "VERSION"
.IX Header "VERSION"
version 1.4.5
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Reads in a fastq file with tradis tags already attached to the start of the sequence
Removes tags from the sequence and quality strings
Outputs a file *.rmtag.fastq unless an out file is specified
.PP
.Vb 1
\&   use Bio::Tradis::RemoveTags;
\&   
\&   my $pipeline = Bio::Tradis::RemoveTags\->new(fastqfile => \*(Aqabc\*(Aq, tag => \*(Aqabc\*(Aq);
\&   $pipeline\->remove_tags();
.Ve
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.SS "Required"
.IX Subsection "Required"
.IP "\(bu" 4
\&\f(CW\*(C`fastqfile\*(C'\fR \- path to/name of file to filter
.IP "\(bu" 4
\&\f(CW\*(C`tag\*(C'\fR \- TraDIS tag to remove
.SS "Optional"
.IX Subsection "Optional"
.IP "\(bu" 4
\&\f(CW\*(C`mismatch\*(C'\fR \- number of mismatches to allow when removing the tag. Default = 0
.IP "\(bu" 4
\&\f(CW\*(C`outfile\*(C'\fR \- defaults to \f(CW\*(C`file.rmtag.fastq\*(C'\fR for and input file named \f(CW\*(C`file.fastq\*(C'\fR
.SH "METHODS"
.IX Header "METHODS"
\&\f(CW\*(C`remove_tags\*(C'\fR \- output all reads with the tags removed to \f(CW\*(C`outfile\*(C'\fR
.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