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2 hours ago by



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
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
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!

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