Hello everybody,
We just launched a nextseq500 run recently.
I analyzed it with Fastqc and I obtained an error at the adapter content plot. It seems like the nextera transposase sequence is too high (see the files).
So I've tried to trim my reads with cutadapt thus I used the following commands because I'm in paired-end :
Python-2.7.9/python ~/cutadapt-1.7.1/bin/cutadapt -q 30 -b CTGTCTCTTATACACATCTGACGCTGCCGACGA --minimum-length 20 --overlap=5 -o tmpl1.1.fastq --paired-output tmpl1.2.fastq myRead_S1_L001_R1_001.fastq myRead_S1_L001_R2_001.fastq
Python-2.7.9/python ~/cutadapt-1.7.1/bin/cutadapt -b CTGTCTCTTATACACATCTCCGAGCCCACGAGAC --minimum-length 20 -q 30 --overlap=5 -o myReads_S1_L001_R2_001.trimmed.fastq --paired-output myReads_S1_L001_R1_001.trimmed.fastq tmpl1.2.fastq tmpl1.1.fastq
And then I checked my results like this :
/FastQC/fastqc myReads_S1_L001_R1_001.trimmed.fastq -t 4 -o FASTQTRY/
Finally I obtained the same plots ! For adapters plots and quality plots as well !
How is that possible ? How can some reads have a quality score less than 30 ?
We just launched a nextseq500 run recently.
I analyzed it with Fastqc and I obtained an error at the adapter content plot. It seems like the nextera transposase sequence is too high (see the files).
So I've tried to trim my reads with cutadapt thus I used the following commands because I'm in paired-end :
Python-2.7.9/python ~/cutadapt-1.7.1/bin/cutadapt -q 30 -b CTGTCTCTTATACACATCTGACGCTGCCGACGA --minimum-length 20 --overlap=5 -o tmpl1.1.fastq --paired-output tmpl1.2.fastq myRead_S1_L001_R1_001.fastq myRead_S1_L001_R2_001.fastq
Python-2.7.9/python ~/cutadapt-1.7.1/bin/cutadapt -b CTGTCTCTTATACACATCTCCGAGCCCACGAGAC --minimum-length 20 -q 30 --overlap=5 -o myReads_S1_L001_R2_001.trimmed.fastq --paired-output myReads_S1_L001_R1_001.trimmed.fastq tmpl1.2.fastq tmpl1.1.fastq
And then I checked my results like this :
/FastQC/fastqc myReads_S1_L001_R1_001.trimmed.fastq -t 4 -o FASTQTRY/
Finally I obtained the same plots ! For adapters plots and quality plots as well !
How is that possible ? How can some reads have a quality score less than 30 ?
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
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