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
A 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?