ATAC-seq Analysis Pipeline with Signac

All preprocessing steps were performed using “Cell Ranger ATAC version 1.2.0” (10X Genomics). Read filtering, alignment, peak calling, and count matrix generation from fastq files were done per sample using ‘cellranger-atac count’. Reference genome assemblies mm10 (refdata-cellranger-atac-mm10–1.2.0) provided by 10xGenomics were used for samples. All further analysis steps were performed in R (Version 4.0.0). Fragments were loaded into R using the package Seurat^{10 (link)}. The R package Signac (version 1.3.0, https://github.com/timoast/signac) was used for normalization and dimensionality reduction. The peak-barcode matrix was then binarized and normalized using the implementation of the TF-IDF transformation described in (RunTFIDF (method = 1)). Subsequently, singular value decomposition was run (RunSVD) on the upper quartile of accessible peaks (FindTopFeatures (min.cutoff = ‘q75’)). The first 20 components from the SVD reduction were used for secondary dimensionality reduction with UMAP.