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:
Does anyones know what the default distance is when classifying alignments as "concordant vs. discordant"?
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)