cell_ranger_arc

Using the filtered single nucleus expression and accessibility matrices, written by Cell Ranger ARC, a Seurat object is prepared that contains RNA and chromatin accessibility assays with little modification.

workflow

Steps

Read Cell Ranger ARC output into assays

Read the Cell Ranger ARC filtered_feature_bc_matrix and save the result, ready to create assay(s). Two RNA assays are created for each dataset: one using features indexed by accession and another by feature name. An additional chromatin accessibility assay is created, for which accession and name are the same since they are genomic intervals.

workflow:L38 R/Seurat/write_10x_counts_matrices R/Seurat/make_assay R/Signac/make_chromatin_assay

Create Seurat object

Collect the miscellaneous data and assays and create a Seurat object, saved as an RDS file.

workflow:L131 R/Seurat/make_object

Printable channels

These channels can be dumped to the output device using the `-dump-channels` Nextflow option with the workflow root tag and the channel tag, for example: seurat:prepare:cell_ranger_arc:tasks.

Tag	Description
`:barcoded_matrices_to_read`	Parameters to read filtered expression matrices in both accession or name modes using.
`:barcoded_matrices`	Paths to the created matrix objects that will be used to write assays.
`:rna_assays_branched.accession`	Paths to assays created using accessions.
`:rna_assays_branched.name`	Paths to assays created using names.
`:rna_assays`	Merge of accession- and name-indexed assays.
`:chromatin_assays_to_create`	Parameters used to make a Signac chromatin accessibility assay.
`:chromatin_assays`	Paths to the created chromatin accessibility assays.
`:objects_to_create`	Parameters used to create Seurat objects.
`:objects`	Paths to created Seurat objects.
`:result`	Input parameters with `seurat path` key added.
`:tasks`	Each task’s output `task.yaml` files from the `task` channel.