Using only .snap file from publication for SnapATAC analysis

[Jasminefighter]

Hi,

I am new to SnapATAC analysis. I'd like to analyze snATAC data from a publication, but only .snap files were provided. The Barcode selection seems to be the first step of the analysis. Could I still proceed with the below analysis if no barcode files were available?

Many thanks,
Jifan

Step 1. Barcode selection
We select high-quality barcodes based on two criteria: 1) number of unique fragments; 2) fragments in promoter ratio;

library(SnapATAC);
x.sp = createSnap(
file="atac_v1_adult_brain_fresh_5k.snap",
sample="atac_v1_adult_brain_fresh_5k",
num.cores=1
);
barcodes = read.csv(
"atac_v1_adult_brain_fresh_5k_singlecell.csv",
head=TRUE
);
barcodes = barcodes[2:nrow(barcodes),];
promoter_ratio = (barcodes$promoter_region_fragments+1) / (barcodes$passed_filters + 1);
UMI = log(barcodes$passed_filters+1, 10);
data = data.frame(UMI=UMI, promoter_ratio=promoter_ratio);
barcodes$promoter_ratio = promoter_ratio;
library(viridisLite);
library(ggplot2);
p1 = ggplot(
data,
aes(x= UMI, y= promoter_ratio)) +
geom_point(size=0.1, col="grey") +
theme_classic() +
ggtitle("10X Fresh Adult Brain") +
ylim(0, 1) + xlim(0, 6) +
labs(x = "log10(UMI)", y="promoter ratio")
p1
barcodes.sel = barcodes[which(UMI >= 3 & UMI <= 5 & promoter_ratio >= 0.15 & promoter_ratio <= 0.6),];
rownames(barcodes.sel) = barcodes.sel$barcode;
x.sp = x.sp[which(x.sp@barcode %in% barcodes.sel$barcode),];
x.sp@metaData = barcodes.sel[x.sp@barcode,];
x.sp