Estimating fragment length from single end data

[intregen]

Hi everyone,

I have single end ATAC-seq data and I want to generate a histogram of the fragment size similar to the one you see in the first figure of most chromatin accessibility papers. I know CollectInsertSizeMetrics from Picard will do this for paired end data, but will it also work for single end data? When I tried running it, it didn't seem to work, but I'm new to bioinformatics so this could be a user error. Many thanks for any help on this you can offer.

[Brian Bushnell]

There's no way to directly calculate the insert size from the mapping information of single-ended data. Sometimes you can infer it based on read position relative to something the fragment is binding to, but that would just be an estimate. I'm not sure if that's possible for ATAC-seq, but I doubt it.