How to use ChromSCape to analyze scATAC-seq data from 10x Genomics？

[zhangdudu0]

I used the cellranger software from 10x Genomics for upstream analysis. I selected the out directory from the cellranger output as the Selected Folder, but a yellow popup window appeared in the bottom right corner, saying that it couldn't find the sparse matrix. I want to ask, what format does this sparse matrix need to be in? It would be even better if you could provide a complete scATAC-seq analysis process using ChromSCape.

[Pacomito]

Dear Zhangdudu, sorry for the delayed answer,

Could you display the naming of the files in the filtered_peak_bc_matrix/ folder ?

When you select the folder, are you correctly selecting lhj7_cellranger-atac/outs/ ? Then in the "Selected samples" display the app should show three folders: _filtered_peak_bcmatrix, _filtered_tf_bcmatrix and _raw_peak_bcmatrix and you have to keep only the _filtered_peak_bcmatrix folder.

Thank you for your suggestion, I will try to make a quick tutorial for scATAC-seq.

Best, Pacôme

[Pacomito]

Dear Zhangdudu,

Did this work ?

I think the function could not read the peaks.bed format from 10X. I modified the code yesterday and tried on a 10X matrix and tested on a 10X dataset, so you might want to give it a try, by re-installing the latest version:

devtools::install_github("vallotlab/ChromSCape").

Best, Pacôme