I have just mapped my ATAC-seq fragments, resulting from paired-end sequencing using this command:
./samtools view file | awk '$9>0' | cut -f 9 | sort | uniq -c | sort -b -k2,2n | sed -e 's/^[ \t]*//' > frag.distribution
I see as expected, a large maximal peak at around 60bp, with most reads under 100bp, and then a second lower hump at around 160-200bp corresponding to the mononucleosome.
However, I also see spikes at 151bp and 139bp - consistent over replicates . You can see similar 'spikes' in the fragment distribution of S. pombe in this paper: "Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions" Figure 3a.
Any idea what these spikes correspond to? Is this related to the fact that Tn5 is a dimer, that inserts two adapters 9bp distance apart?