debian man page for fastq_masker

FASTQ_MASKER(1) 						   User Commands						   FASTQ_MASKER(1)

NAME
       fastq_masker - Masks nucleotides with 'N' (or other character) based on quality

DESCRIPTION
       usage: fastq_masker [-h] [-v] [-q N] [-r C] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu)

       [-h]   = This helpful help screen.

       [-q N] = Quality threshold - nucleotides with lower quality will be masked

	      Default is 10.

       [-r C] = Replace low-quality nucleotides with character C. Default is 'N'

       [-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_masker 0.0.13.2						     May 2012							   FASTQ_MASKER(1)