Based on your experience, at which point would you recommend merging the reads from multiple ATAC-seq replicates (biological replicates, for the most part)? And most importantly, why?
I saw at Encode they first process the samples independently up to the BAM files, and merge all BAM files using samtools. What would you lose/gain by merging reads at the fastq level? Or would you rather ignore all of this and merge the results at the very end of the pipeline? (say, after you've called peaks on each of these samples independently) My intuition suggests to merge these files right after trimming reads, but I'm curious about the reasoning for your choice of merge step.
Thanks for any feedback!