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.

[紫枫]

I have the same problem. I downloaded a single-end ChIP-seq data. No matter what I use --ATACshift or --shift 4-5, the output file reads count is 0. I couldn't find any description about SE data on the GitHub page of deeptools. Maybe alignmentSieve doesn't support SE data.

[ATpoint]

ChIP-seq and shifting have nothing to do with each other. Also, motif discovery, e.g. with meme or homer do not require it.