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  • fastq_quality_filter -p 100 or could be less?

    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

  • #2
    Q17 is a pretty strenuous threshold, you might try 5, or better yet just do regular trimming and discard anything too short to map.

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