Some trouble with the FastQC report

[Citrusyh]

Hi Felix, I am sorry to trouble you. I’m having some trouble with the FastQC report and would like to ask you.

1. According to the “Per base sequence content”, should I clip the first 6 bp for good results? And this curve doesn’t look smooth.
2. According to the “Sequence Duplication Levels”, why is there only one line here? What’s wrong with my code?
3. There are so many overrepresented sequences, is it normal when dealing with RRBS data? I had input code like this:
4. trim_galore trim_galore -q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired A61.1.fq.gz A61.2.fq.gz -o /export/home/***
5. fastqc fastqc -o /export/home/limiao29/RRBS/Lung/fastqc -t 12 /export/home/limiao29/RRBS/Lung/*.fq.gz