Hi everyone, thank you for sharing the ATAC-seq pipeline! I’m very new to Nextflow and ATAC-seq, and I have a simple question. My goal is to analyse data from multiple species (mouse, human), and I wonder when and how to join the data. Should I run the pipeline separately for each species and combine two datasets after peak calling (before/after MACS2), or at some other step? Sorry for a basic question. I’d appreciate your help.

Hi Amir, That depends on what you actually want to do. The short answer is, you will need to run the pipelines for each species separate. Then you can do follow up analysis on what ever you want to do, not entirely sure what your objectives are, difficult to give a concrete advice for that part.

Hi Kevin, thank you for your reply! My goal is to compare chromatin accessibility between human and other species in a specific gene promoter. I thought with ATAC-seq we can get a final table, like gene expression in RNA-seq 😅 Sorry for a basic question; I’ll read the docs and let you know if I have more questions

Hi Amir, Never mind, not a stupid question at all. A simple, and likely not sufficient, starting point could be to run the atac seq pipeline for individual species and check in a genome browser the obtained atac-signal and peaks at your orthologs of interest. However, doing those cross species comparisons genome wide is more tricky and I’m likely not the best person to give you advice on that. Naively, you could try to liftover coordinates from one species to another (check UCSC tools) and compare those or you will need to dig a bit deeper in some synteny based analysis but this would all be downstream of the atac seq pipeline.

Got it, thank you very much! Will do!!