Hi,
I have a problem regarding adapter clipping. After combined soft trimming and adapter clipping, fastQC still detects adapters as overrepresented sequences. I've created a test file with just the related adapter (Illumina, 5p, index11), but the output says "counted 0". I even tried "-t 0", as it occurs just 15-20% instead of 25%. What could be the reason? And what is the difference between "counted 0" and "no adapters found"?
The command was fastq-mcf -o file_trim.fastq -t 0 -l 20 -q 20 -P 33 -S file_adapters.fasta file_sample.fastq >| trim_output.log
Many thanks in advance!
I have a problem regarding adapter clipping. After combined soft trimming and adapter clipping, fastQC still detects adapters as overrepresented sequences. I've created a test file with just the related adapter (Illumina, 5p, index11), but the output says "counted 0". I even tried "-t 0", as it occurs just 15-20% instead of 25%. What could be the reason? And what is the difference between "counted 0" and "no adapters found"?
The command was fastq-mcf -o file_trim.fastq -t 0 -l 20 -q 20 -P 33 -S file_adapters.fasta file_sample.fastq >| trim_output.log
Many thanks in advance!