Hello,
I would appreciate any thoughts on this. In the FastQC report on my Illumina PE reads, the Per base N content is 0 while in the overrepresented sequences I have Ns. I haven't come across any discussion in Biostars or any where else where the overrepresented sequences are Ns. Can anybody explain why this could be and what I need to do about it. Thank you.
Edit: here are the links to the Per base N content and overrepresented sequence report from FastQc:
Can you post the relevant output somewhere so we can have a look?