fastq_quality_filter -p 100 or could be less?

[Sergio.pv]

Hello everyone,
I am using FASTX-toolkit to filter my data (small RNA fraction for miRNA analyses) according to quality.
I use the following settings:
fastq_quality_filter -v -q 17 -p 100 -Q 33

This means, that the output will consist in reads where 100% nucleotides are >=17 phred score.

However, when doing that I loss a big amount of reads. For example:
Quality cut-off: 17
Minimum percentage: 100
Input: 95428 reads.
Output: 29635 reads.
discarded 65793 (68%) low-quality reads.

My question is, whether is there a safe trade off between using lower minimum pecentage and still having a good file for mapping.

Thanks in advance

[dpryan]

Q17 is a pretty strenuous threshold, you might try 5, or better yet just do regular trimming and discard anything too short to map.