Read the doc ! ;)
usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.13 by A. Gordon (email@example.com)
[-h] = This helpful help screen.
[-q N] = Minimum quality score to keep.
[-p N] = Minimum percent of bases that must have [-q] quality.
[-z] = Compress output with GZIP.
[-i INFILE] = FASTA/Q input file. default is STDIN. //------- HERE -------
[-o OUTFILE] = FASTA/Q 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.
Your line must contain "-i" if you want to read from a file (or using "|" (pipe) from other program's output):
fastq_quality_filter -q 30 -p 99 -i /media/azhar/785A3A155A39D11C/MouseTissueChIP/MouseYH2mBulblc/IgG_KD17060333_H35FLCCXY_L4_1.fq -o /media/azhar/785A3A155A39D11C/MouseTissueChIP/IgGfiltered.fq
modified 3.4 years ago
3.4 years ago by
glihm • 620