Question: Fastx tools no output?
0
gravatar for Azhar
3.4 years ago by
Azhar50
China
Azhar50 wrote:

Hi I am trying to use Fastx tools but after running for long time even whole no out put on shell also no output after many ours no running is shown no error just blank screen I used fastx trimmer and quality filter. For fastq quality filter the code which i used is below

fastq_quality_filter -q 30 -p 99 /media/azhar/785A3A155A39D11C/MouseTissueChIP/MouseYH2mBulblc/IgG_KD17060333_H35FLCCXY_L4_1.fq -o /media/azhar/785A3A155A39D11C/MouseTissueChIP/IgGfiltered.fq
chip-seq • 1.2k views
ADD COMMENTlink modified 3.4 years ago by glihm620 • written 3.4 years ago by Azhar50
2
gravatar for glihm
3.4 years ago by
glihm620
France
glihm620 wrote:

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 (gordon@cshl.edu)

   [-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
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by glihm620
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