trim_fastq.pl - Trim sequence and quality string of fastq files on the fly
trim_fastq.pl [-f FILE] [-u INTEGER] [-d INTEGER] [-a5 STRING] [options]
This program trims sequence and qualitystring fields from a fastq file, either by a number of nucleotides, or by removing a user defined 5' adapter sequence. The typical usage scenario is to allow re-mapping if mapping quality is not sufficient without trimming.
Fastq file for trimming
Number of nucleotides to trim from read / quality string start
Number of nucleotides to trim from read / quality string end
Sequence of 5' adapter to trim from the left side of the reads. This option and -u / -d are mutually exclusive
Print short help
Prints the manual page and exits
Joerg Fallmann <joerg.fallmann@univie.ac.at> Michael T. Wolfinger <michael@wolfinger.eu>
2 POD Errors
The following errors were encountered while parsing the POD:
Unknown directive: =over1
'=item' outside of any '=over'
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ViennaNGS
CPAN shell
perl -MCPAN -e shell install Bio::ViennaNGS
For more information on module installation, please visit the detailed CPAN module installation guide.