NAME

fastQ_brew - a modern module for preprocessing of fastQ formatted files

DESCRIPTION

Provides methods for filtering and trimming reads by length and quality.

FEEDBACK

damienoh@gwu.edu

Mailing Lists

User feedback is an integral part of the evolution of this module. Send your comments and suggestions preferably to one of the mailing lists. Your participation is much appreciated.

Support

Please direct usage questions or support issues to: <damienoh@gwu.edu> Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the GitHub bug tracking system to help keep track of the bugs and their resolution. Bug reports can be submitted via the GitHub page:

https://github.com/dohalloran/fastQ_brew/issues

AUTHORS - Damien OHalloran

Email: damienoh@gwu.edu

APPENDIX

The rest of the documentation details each method

fastQ_brew->new_with_options()

Function: Populates the user data into $self 
Returns : nothing returned
Args    :
 --i, input file (required)
 --o, output file (required)
 --lib, library type  (default is sanger)       
 --dup, remove duplicate reads
 --qf, filter by phred (quality)
 --dist, standard deviations between min and mean Q score permitted
 --lf, filter by read length
 --trim_l, trim reads starting at left end
 --trim_r, trim reads starting at left end
 --adpt, remove a user supplied adapter     
 --fasta, convert to fastA format 
 --dna_rna, convert reads to RNA
 --rev_comp, reverse complement reads
 --no_n, remove non-designated bases from reads
 --help, Print this help

truseq adapters

>TruSeq_Universal_Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >TruSeq_Adapter_Index_1_6 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_2 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_3 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_4 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_5 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_6 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_7 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_8 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_9 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_10 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_11 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_12 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_13 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_14 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCGTATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_15 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_16 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCGATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_18_7 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCACATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_19 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_20 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_21 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_22 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTAATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_23 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_25 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATATCTCGTATGCCGTCTTCTGCTTG >TruSeq_Adapter_Index_27 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTATCTCGTATGCCGTCTTCTGCTTG

run_fastQ_brew()

Title   : run_fastQ_brew()
Usage   : $self->run_fastQ_brew(%arg)
Function: option to filter reads
Returns : filtered fastQ file
Args    : $self, %arg

_cleanup()

Title   : _cleanup()
Usage   : _cleanup(%arg);
Function: delete tmp files
Returns : nothing
Args    : %arg

LICENSE AND COPYRIGHT

Copyright (C) 2017 Damien M. O'Halloran
GNU GENERAL PUBLIC LICENSE