ATAC seq enhancer help

Question

[mrs.whirly]

Hello everyone,

I am analyzing ATAC-seq data to identify enhancers. This is my first time doing this particular analysis. I am using Bowtie2 to align the raw sequencing data. I used their default settings for paired-end reads. I have two questions:

1. Does anyones know what the default distance is when classifying alignments as "concordant vs. discordant"?
2. What the ATAC seq fragments sizes usually are with respect to enhancers? (to see if their default size setting is actually in line with what I want to see in this case)

[ATpoint]

1) It should be the default value of the -X parameter in bowtie2.

2) No preference afaik. Enhancers have nucleosome-free regions and histone signals like many other open regions. I do not see how you could identify enhancers purely based on ATAC-seq. You would need functional data to demonstrate activating functions towards the target genes or at least ChIP-seq data for activating histone marks. Not every open and non-promoter region is an enhancer.