Hi

I am new to ATAC-Seq and ChIP-Seq and I have a question on removing duplicates when it comes to paired-end ATAC-Seq and paired-end ChIP-Seq pipelines.

I have seen some papers where clumpify is used in the first step to remove duplicates followed by bwa-mem and passing the bam files (after shifting for ATAC-Seq) to MACS2 with no usage of Picard MarkDuplicates.

https://www.cell.com/cell-genomics/pdf/S2666-979X(23)00019-8.pdf
Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements
ChIP-seq analysis
Prior to analysis, reads were processed to remove optical duplicates with clumpify (BBMap v38.20; https://sourceforge.net/projects/
bbmap/) [dedupe = t optical = t dupedist = 2500]

I have seen this post - Did you remove ChIP-seq duplicates - where Picard MarkDuplicates is used

Hence just curious - is there benefits with one approach or the other (Approach 1 - using clumpify as step 1 and no MarkDuplicates; Approach 2 - use aligned bam files and then do MarkDuplicates)

If using clumpify, is the above correct - dedupe=t optical=t dupedist=2500

• Removing fastq duplicates GenoMax suggests hdist=0 for making it strict
• Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneous tools should I use dedupe=t optical=f or dedupe=t optical=t

I would like to seek your advice and guidance on the above for both ATAC-Seq and ChiP-Seq.

• Would anything change if it was single-end instead of paired-end as alluded to here: Did you remove ChIP-seq duplicates

Thanks in advance.