The 4DN ATAC-seq data processing pipeline uses the ENCODE ATAC-seq pipeline v1.1.1. We have modified the logistics of the pipeline execution without changing the content of the pipeline.
We have split the pipeline into two sub-pipelines; 1) alignment and filtering and 2) peak calling. A quality control report is generated at each step.
For certain cases, we add a replicate-merging step between the two steps (not a part of the ENCODE pipeline). * If an experiment set has >1 biological replicates and >1 technical replicates in a biological replicate, we merge the technical replicates.
We perform the basic QC that comes with the ATAC-seq pipeline, but we do not perform ATAQC, an additional QC that requires a set of reference files that do not yet have official release/documentation, i.e. we use the flag
For more detail, see description/documentation from ENCODE.