Fastq_quality_filter no removing sequences

[oneofmany]

Hello everyone,
I am trying to filter some fastq files based on the quality scores obtained by fastqc. However after running fastq_quality_filter from the fastx tools I realized that there are not removed sequences in the outpout file. Somehow, the program is not cleaning the original file.

My commands:
$ fastq_quality_filter -Q28 -p 100 -i input.fastq -o output.fastq

Any suggestions? Could it be a encoding issue? my files are in Sanger Illumina 1.9 encoding

Thank you for any help

[kmcarr]

I think you are confusing arguments.

'-Q' defines the ASCII quality offset, which for Illumina 1.9 is 33. FastX toolkit still defaults to 64 if you do not specify -Q.

The argument to set the minimum Q-score to test for in fastq_quality_filter is '-q'. The correct command based on what you have above would be

# fastq_quality_filter -Q 33  -q 28 -p 100 -i input.fastq -o output.fastq

Do you really want to discard any read which has a single base with a Q score below 28?

[oneofmany]

Thank you that makes more sense.
Now that I think about it I can loose a little the restriction of the filtering.
Thanks again.