Downstream analysis during sc-ATAC seq

Question

[applepie]

Hi, I have been analysisg a single-cell ATAC seq data published in a Cell Paper titled "Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer" (DOI: 10.1016/j.ccell.2021.09.010), and I have retrieved the ATAC seq data from the GEO(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169246). I realised that the ATAC-seq data is encoded in the format of feature-bacode matrix (See the attached photo)

However, How can we do the dow sc-ATAC seq analysis if the file loaded in is not h5 file? Becoz usually the tutorials online teach us to load in h5 files using Read10X_h5. (For example: https://stuartlab.org/signac/articles/pbmc_vignette)

Answer 1

[Ming Tommy Tang]

read the counts.mtx file using readMM from the Matrix R package, and the barcode and feature file are just tsv file. you can then make a Seruat object after you read them into R.

See example here for single-cell RNAseq https://divingintogeneticsandgenomics.com/post/reuse-the-single-cell-data-how-to-create-a-seurat-object-from-geo-datasets/ but it is similar to scATAC

[applepie]

Thanks for your reply.

But when I tried to load in the feature-barcode matrix, there was no Fragment file here. I actually wanna run CreatechromatinAssay() before any conversion into Seurat object.

I followed this website to do my sc-ATAC seq analysis: https://stuartlab.org/signac/articles/pbmc_vignette.html

They create seurat object using the following code: