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)