We run ATAC samples that are not in distinct experimental groups (no replicates) but still would like to make a comparison between the number of reads of each sample in the consensus peaks. However, currently this is not possible because the featureCounts step that does this analysis is coupled to the DESeq2 analysis, which is skipped in the absence of replicates. It would be helpful to separate the two processes, so that the featureCounts step can still be run even if DESeq2 is skipped.