Atac-seq shift single-end data

Question

[sarahmanderni]

Hi,

Atac-seq +4 -5 shift is required when aiming for nucleotide resolution analysis (e.g. TF motif discovery). The available tools (e.g. alignmentSieve from deeptools) look for properly paired reads and perform the shifting. Can this idea anyhow be applied to the single-end data? I know single-end is way far from optimal but this is what I have at the moment.