Quality control of single-cell ATAC-seq data without peak calling using Chromap
Ahmed, O.; Zhang, H.; Langmead, B.; Song, L.
Show abstract
In this work, we extend Chromap, an ultrafast method for single-cell ATAC-seq data alignment, to directly report peak-based quality control (QC) metrics, such as the fraction of reads in peaks, without calling peaks. Recent single-cell ATAC-seq analysis methods like SnapATAC2 utilize the genome-interval-based feature for data analysis, which disables filtering low-quality cells using common peak-based QC metrics. We show that Chromaps QC metrics capture additional low-quality cells missed by SnapATAC2 and improve downstream analysis results without sacrificing computational efficiency.
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