ATAC-Seq kmer removal

Question

[elenichri]

Hello,

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 https://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!

Answer 1

[ATpoint]

To be honest I would not even care about it. I suggest you map your data and then see if there is anything odd during downstream analysis. If not ignore it.

[elenichri]

Actually, this is what I have been thinking, after discussing with some colleagues too..I already mapped and I have mapping rate 96-97%, which is very good! Thanks for the reply.