Cell Ranger ARC1.0, printed on 10/04/2023
The atac_cut_sites.bigwig file contains a track of the smoothed transposition sites across the genome. Each unique ATAC-seq fragment contributes two transposition events, one for each end of the fragment. As described in the fragment file documentation, the cut sites are adjusted relative to the read alignment positions to account for the 9bp overhang of the transposase cut site behavior. A count of the total number of transposition events across all fragments with all barcodes is kept for every position in the genome.
The raw cut sites are are relatively sparse and subject to local variation in transposase affinity. For easier interpretation and use, we report smoothed rather than raw cut site counts. The smoothed counts report the total number of tagmentation cut sites within a fixed window of -200bp to +200bp around each genomic position. This smoothed signal is how the signal track for peak calling is thresholded, and can be used to investigate peak caller results.
The pipeline outs/ folder contains a single atac_cut_sites.bigwig. This file is output in the indexed binary bigWig format. It is suitable for direct loading into the Integrative Genome Viewer for visualization. It can also be accessed using UCSC's binary utilities or with the Python pyBigWig package.