The difference of Peak/Cell matrix and TSS usage

[beginner984]

Hello

I need your help please to understand this

Cell-ranger atac pipeline returns two files filtered_peak_bc_matrix.h5 and filtered_tf_bc_matrix.h5

Extract which from fragment file?

Signac software uses Peak/Cell matrix by getting filtered_peak_bc_matrix.h5

What if in your software I use Peak/Cell matrix instead?

My question please is, does your sofware tries TSS enrichment and Signac package uses something equivalent to gene expression in transcriptome?

Thank you so much for any help

[rcorces]

I would encourage you to read the manual, publication, and supplementary material from the publication in full before posting questions.

Cell-ranger atac pipeline returns two files filtered_peak_bc_matrix.h5 and filtered_tf_bc_matrix.h5

ArchR does not use either of these files.

What if in your software I use Peak/Cell matrix instead?

This is not possible in ArchR.