scATAC-Seq Examples

Below are different examples of setting up workflows for scATAC-Seq experiments. For general configuration details, refer to Configuration details.

Multiple samples

samples.tsv

sample   replicate genome HDF5_Multiple_Assays RDS_Multiple_Assays Gene.Expression Peaks                                       TF                                       fragments                          singlecell                 meta_batch  meta_tissue
CTX                mm10                                                            CTX_rerun/outs/filtered_peak_bc_matrix.h5   CTX_rerun/outs/filtered_tf_bc_matrix.h5  CTX_rerun/outs/fragments.tsv.gz    CTX_rerun/outs/summary.csv batch1      CTX
MGE                mm10                                                            MGE_rerun/outs/filtered_peak_bc_matrix.h5   MGE_rerun/outs/filtered_tf_bc_matrix.h5  MGE_rerun/outs/fragments.tsv.gz    MGE_rerun/outs/summary.csv batch1      MGE

Note

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

$ tree filtered_peak_bc_matrix
filtered_peak_bc_matrix
├── barcodes.tsv
├── matrix.mtx
└── peaks.bed

Multiple samples, aggregated

samples.tsv

sample  replicate  genome  HDF5_Multiple_Assays    RDS_Multiple_Assays   Gene.Expression Peaks                                      TF      fragments                           singlecell                      meta_batch
aggr               mm10                                                                  aggr_rerun/outs/filtered_peak_bc_matrix.h5         aggr_rerun/outs/fragments.tsv.gz    aggr_rerun/outs/singlecell.csv  batch1

aggregates.tsv

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

Technical Replicates (Uncommon)

samples.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_peak_bc_matrix/      pbmc1/outs/fragments.tsv.gz             batch1      wt
ipsc   A         hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      ipsc/outs/fragments.tsv.gz              batch1      wt
pbmc2  A         hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      pbmc2/outs/fragments.tsv.gz             batch1      wt
pbmc1  B         hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      pbmc1/outs/fragments.tsv.gz             batch1      wt
ipsc   B         hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      ipsc/outs/fragments.tsv.gz              batch1      wt
pbmc2  B         hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      pbmc2/outs/fragments.tsv.gz             batch1      wt

Custom assays (Uncommon)

samples.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_peak_bc_matrix/      pbmc1/outs/fragments.tsv.gz             batch1      wt
ipsc             hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      ipsc/outs/fragments.tsv.gz              batch1      wt
pbmc2            hg38                                                            pbmc1/outs/filtered_peak_bc_matrix/      pbmc2/outs/fragments.tsv.gz             batch1      wt

assays.tsv

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