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fastq_quality_trimmer(1) [debian man page]

FASTQ_QUALITY_TRIMMER(1)					   User Commands					  FASTQ_QUALITY_TRIMMER(1)

NAME
fastq_quality_trimmer - Filters sequences based on quality DESCRIPTION
usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gor- don@cshl.edu) [-h] = This helpful help screen. [-t N] = Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence). [-l N] = Minimum length - sequences shorter than this (after trimming) will be discarded. Default = 0 = no minimum length. [-z] = Compress output with GZIP. [-i INFILE] = FASTQ input file. default is STDIN. [-o OUTFILE] = FASTQ output file. default is STDOUT. [-v] = Verbose - report number of sequences. If [-o] is specified, report will be printed to STDOUT. If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR. SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit http://hannonlab.cshl.edu/fastx_toolkit/commandline.html to get a better layout as well as an overview about connected FASTX tools. fastq_quality_trimmer 0.0.13.1 April 2012 FASTQ_QUALITY_TRIMMER(1)

Check Out this Related Man Page

FASTA_FORMATTER(1)						   User Commands						FASTA_FORMATTER(1)

NAME
fasta_formatter - changes the width of sequences line in a FASTA file DESCRIPTION
usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e] Part of FASTX Toolkit 0.0.13.2 by gordon@cshl.edu [-h] = This helpful help screen. [-i INFILE] = FASTA/Q input file. default is STDIN. [-o OUTFILE] = FASTA/Q output file. default is STDOUT. [-w N] = max. sequence line width for output FASTA file. When ZERO (the default), sequence lines will NOT be wrapped - all nucleotides of each sequences will appear on a single line (good for scripting). [-t] = Output tabulated format (instead of FASTA format). Sequence-Identifiers will be on first column, Nucleotides will appear on second column (as single line). [-e] = Output empty sequences (default is to discard them). Empty sequences are ones who have only a sequence identifier, but not actual nucleotides. Input Example: >MY-ID AAAAAGGGGG CCCCCTTTTT AGCTN Output example with unlimited line width [-w 0]: >MY-ID AAAAAGGGGGCCCCCTTTTTAGCTN Output example with max. line width=7 [-w 7]: >MY-ID AAAAAGG GGGTTTT TCCCCCA GCTN Output example with tabular output [-t]: MY-ID AAAAAGGGGGCCCCCTTTTAGCTN example of empty sequence: (will be discarded unless [-e] is used) >REGULAR-SEQUENCE-1 AAAGGGTTTCCC >EMPTY-SEQUENCE >REGULAR-SEQUENCE-2 AAGTAGTAGTAGTAGT GTATTTTATAT SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit http://hannonlab.cshl.edu/fastx_toolkit/commandline.html to get a better layout as well as an overview about connected FASTX tools. fasta_formatter 0.0.13.2 May 2012 FASTA_FORMATTER(1)
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