Hi, after trimming bad quality ends and the primers with cutadapt I am using usearch to do some quality filltering with this little script:
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
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
someone knows the meaning?
could it have something to do with the steps that I take in cutadapt? thanks a lot for any help