This is the command fastq_masker that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 0.0.14 by A. Gordon (assafgordon@gmail.com)
[-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.
Use fastq_masker online using onworks.net services