09-28-2014
You have shown output you do not want. This is not generally helpful. It's difficult to guess what a broken program we've never seen before is supposed to be doing.
How about showing us what output you do want? That would be very helpful. Much less wild-guessing.
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Networking in nature
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LEARN ABOUT DEBIAN
fastq_quality_trimmer
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)