I am analyzing bulk paired end ATAC-Seq data. Initial fastqc shows kmers and adapter content. I trim the adapters with cutadapt and run fastqc to check if they are properly removed. They are, indeed. However, I have a high kmer content at the beginning of all my sequences, in all my samples (I have 14 samples) see here ibb.co/crHVFRd
I use the command
cutadapt -O 13 -a CTGTCTCTTATACACATCTNNNNNNNNNN -A CTGTCTCTTATACACATCTNNNNNNNNNN -q 20 --minimum-length 36 -o ..........
to remove additional 10bp after adapter removal. The results image is ibb.co/m4P6pZx
I have two questions:
1) Why the length of the sequence is not trimmed?Why do I still have 150bp?
2) The kmer content is still there art the beginning of the sequence and I have additional kmers at the end. Why does this happen?
Thank you very much!