table of contents
Bio::Tradis::RemoveTags(3pm) | User Contributed Perl Documentation | Bio::Tradis::RemoveTags(3pm) |
NAME¶
Bio::Tradis::RemoveTags - Remove tags from seqs a fastq file
VERSION¶
version 1.4.5
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
use Bio::Tradis::RemoveTags; my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc'); $pipeline->remove_tags();
PARAMETERS¶
Required¶
- "fastqfile" - path to/name of file to filter
- "tag" - TraDIS tag to remove
Optional¶
- "mismatch" - number of mismatches to allow when removing the tag. Default = 0
- "outfile" - defaults to "file.rmtag.fastq" for and input file named "file.fastq"
METHODS¶
"remove_tags" - output all reads with the tags removed to "outfile"
AUTHOR¶
Carla Cummins <path-help@sanger.ac.uk>
COPYRIGHT AND LICENSE¶
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
2024-01-25 | perl v5.38.2 |