Question for Signac Package Tutorial
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Entering edit mode
7 months ago
yzhao140 • 0

Hello, everyone. I am learning to use Signac to analyze scATAC-seq data.I went through the workflow of this tutotial(PBMC dataset in 10X Genomics)(https://satijalab.org/signac/articles/pbmc_vignette.html) . For counts variable(peak by cell matrix) created by Signac, I found that there are entries that can larger than 2. But as far as I know, the maximal value of scATAC-seq count data should less than 2? I also attached the code in this thread.

library(Signac)
library(Seurat)
library(GenomeInfoDb)
library(EnsDb.Hsapiens.v75)
library(ggplot2)
library(patchwork)
library(hdf5r)
set.seed(1234)

counts = Read10X_h5(filename = "atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5")
metadata = read.csv(
  file = "atac_v1_pbmc_10k_singlecell.csv",
  header = TRUE,
  row.names = 1
)

head(counts)
R scATAC-seq PBMC • 248 views
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