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Old 11-07-2017, 01:39 AM   #1
ireneirene
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Location: netherlands

Join Date: Nov 2017
Posts: 3
Default 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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