scRNA-Seq Examples

Below are different examples of setting up workflows for scRNA-Seq experiments. For general configuration details, see Configuration details.

Multiple samples

sample.tsv

sample replicate genome HDF5_Multiple_Assays RDS_Multiple_Assays Gene.Expression                        Peaks   TF  fragments singlecell  meta_batch meta_tissue
CTX              mm10                                            CTX/outs/filtered_feature_bc_matrix.h5                                   batch1     CTX
MGE              mm10                                            MGE/outs/filtered_feature_bc_matrix.h5                                   batch1     MGE

Note

Alternatively, the Gene.Expression column can point to a directory (e.g. path/to/outs/filtered_feature_bc_matrix/) containing a MEX format sparse matrix along with barcodes and features, as shown below:

$ tree filtered_feature_bc_matrix
filtered_feature_bc_matrix
├── barcodes.tsv.gz
├── features.tsv.gz
└── matrix.mtx.gz

Multiple samples, aggregated

sample.tsv

sample  replicate  genome  HDF5_Multiple_Assays    RDS_Multiple_Assays     Gene.Expression Peaks                          TF      fragments       singlecell    meta_batch
aggr               mm10                                                    aggr/outs/count/filtered_feature_bc_matrix.h5                                        batch1

aggregates.tsv

sample replicate library_id bc_suffix meta_tissue
CTX              1          1         CTX
MGE              2          2         MGE

Technical Replicates (Uncommon)

sample.tsv

sample replicate genome HDF5_Multiple_Assays RDS_Multiple_Assays Gene.Expression                          Peaks TF fragments singlecell  meta_batch  meta_geno
pbmc1  A         hg38                                            pbmc1/outs/filtered_feature_bc_matrix.h5                                batch1      wt
ipsc   A         hg38                                            ipsc/outs/filtered_feature_bc_matrix.h5                                 batch1      wt
pbmc2  A         hg38                                            pbmc2/outs/filtered_feature_bc_matrix.h5                                batch1      wt
pbmc1  B         hg38                                            pbmc1/outs/filtered_feature_bc_matrix.h5                                batch1      wt
ipsc   B         hg38                                            ipsc/outs/filtered_feature_bc_matrix.h5                                 batch1      wt
pbmc2  B         hg38                                            pbmc2/outs/filtered_feature_bc_matrix.h5                                batch1      wt

Custom assays (Uncommon)

sample.tsv

sample replicate genome HDF5_Multiple_Assays RDS_Multiple_Assays Gene.Expression                          Peaks TF fragments singlecell  meta_batch  meta_geno
pbmc1            hg38                                            pbmc1/outs/filtered_feature_bc_matrix.h5                                batch1      wt
ipsc             hg38                                            ipsc/outs/filtered_feature_bc_matrix.h5                                 batch1      wt
pbmc2            hg38                                            pbmc2/outs/filtered_feature_bc_matrix.h5                                batch1      wt

assays.tsv

sample replicate assay.name path
pbmc1
ipsc             enhancer   pbmc1/assays/enhancer_bc_matrix.h5
pbmc1