Fastx toolkits: fastq_quality_filter does not discart any read

Question

[DVR]

Hello All,

I made a quality plot and now I would like to remove reads with a quality less than 25. I ran

fastq_quality_filter -q 35 -v -i U/Seqs/R1.fastq -o U/forward_filter_35

And I got:

Quality cut-off: 25
Minimum percentage: 0
Input: 11781134 reads.
Output: 11781134 reads.
discarded 0 (0%) low-quality reads.

I try with a higher filter (-q 35) and also I had 0 reads discarded. Do anybody know what is happening?

Thanks!

[apelin20]

Is this Phred 60? illumina encoding? or perhaps phred 33 (in which case add -Q 33 at the end of the command line)?

Answer 1

[zorbax]

It's just -Q33 without space.