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  • ireneirene
    Junior Member
    • Nov 2017
    • 3

    quality filtering error usearch

    Hi, after trimming bad quality ends and the primers with cutadapt I am using usearch to do some quality filltering with this little script:

    Code:
    for fq in out_trimmed/*_trimmed_primers2.fastq do usearch9 -fastq_filter $fq -fastq_maxee 1 -fastq_minlen 200 -fastaout "${fq%.fastq}.fa" done
    but I get this error: e../fastqfilter.cpp(132) assert failed: Qual != 0

    someone knows the meaning?

    could it have something to do with the steps that I take in cutadapt? thanks a lot for any help

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