I have trouble interpreting the CollectMultipleMetrics.base_distribution_by_cycle plot from picard for atac-seq data
In my example, there's weird patterns at what looks like the begining of each paired end sequence. Is it a direct reflection of tthe fastqc sequence content across all bases? I am worried about adapter contamination but the picard plot is the same with out without adapter removal.
The picard plot:
The fastqc plot:
Can I just take to heart this post about the fastqc metric and call it a day ?