I have 8 PRO-seq samples which all have very similar k-mer plots (one of them: http://pasteboard.co/xuO4V7O.png). At the start of the reads they have very high enrichment.
The used adapter is TGGAATTCTCGGGTGCCAAGG, which has been removed using CutAdapt. I don't know how to go from here to find where this k-mer enrichment comes from. Are there any tools available to go deeper into this, or do you have any suggestions where these enriched k-mers could come from?
I just realized that I have been reading the plot incorrectly. Seems only the first 4 bases are enriched, not the complete k-mers.