Hello,
Thanks for the useful software. I'm using the supercell-2.0 branch, and just formed metacells with SCimplify_for_Seurat(). It may be useful to have the original ATAC fragments downstream, but my input Seurat object is composed of multiple samples (i.e. has multiple fragment files), and as far as I understand AggregateFragmentFile() doesn't support this case, does it? As a recommendation (if I'm understanding correctly), it might be most straightforward to have an AggregateFragments() function whose input is Fragments(cell_level_seurat_obj[[ATAC_assay]]) (and a membership vector) rather than looking for the original file(s), which may be quite complex to handle for a multi-sample object. Thanks!
Best,
-Nick
Hello,
Thanks for the useful software. I'm using the
supercell-2.0branch, and just formed metacells withSCimplify_for_Seurat(). It may be useful to have the original ATAC fragments downstream, but my input Seurat object is composed of multiple samples (i.e. has multiple fragment files), and as far as I understandAggregateFragmentFile()doesn't support this case, does it? As a recommendation (if I'm understanding correctly), it might be most straightforward to have anAggregateFragments()function whose input isFragments(cell_level_seurat_obj[[ATAC_assay]])(and a membership vector) rather than looking for the original file(s), which may be quite complex to handle for a multi-sample object. Thanks!Best,
-Nick