Output Files

Most output files contain a header summarizing the pipeline run. Headers contain all of the information needed to rerun the pipeline with the same settings.

Outputs for all pipeline runs:

Output	File	Content
Metrics summary	[sample_name]_Metrics_Summary.csv	Report containing sequencing, molecules, and cell metrics
Pipeline report HTML	[sample_name]_Pipeline_Report.html	Summary report containing the results from the sequencing analysis pipeline run
Data tables (See a. and b. below)	[sample_name]_RSEC_MolsPerCell_MEX.zip [sample_name]_DBEC_MolsPerCell_MEX.zip	Molecules per bioproduct per cell, based on RSEC or DBEC
Unfiltered Data table	[sample_name]_RSEC_MolsPerCell_Unfiltered_MEX.zip	Unfiltered tables containing all cell labels with ≥10 reads
BAM and BAM Index (if parameter is set)	[sample_name]_Bioproduct.bam [sample_name]_Bioproduct.bam.bai	Alignment file of R2 with associated R1 annotations for Bioproduct
Single-cell analysis tool inputs	[sample_name]_Seurat.rds [sample_name].h5mu	Seurat (.rds) input file containing RSEC molecules data table and all cell annotation metadata. Scanpy / Muon input file containing RSEC molecules data table and all cell annotation metadata.
Bioproduct Statistics	[sample_name]_Bioproduct_Stats.csv	Metrics from RSEC and DBEC Unique Molecular Identifier adjustment algorithms on a per-bioproduct basis
Dimensionality Reduction	[sample_name]_(assay)_tSNE_coordinates.csv [sample_name]_(assay)_UMAP_coordinates.csv	Dimensionality reduction coordinates per cell index
Immune cell classification	[sample_name]_(assay)_cell_type_experimental.csv	Immune cell type prediction per cell index

(a) For a multiplexed samples run, theses tables contain counts for putative cells from all samples combined.
(b) DBEC data table is only output if the experiment includes targeted mRNA or AbSeq bioproducts

Outputs when multiplex option selected:

Output	File	Content
Sample Tags metrics	[sample_name]_Sample_Tag_Metrics.csv	Metrics from the sample determination algorithm
Sample Tag calls	[sample_name]_Sample_Tag_Calls.csv	Assigned Sample Tag for each putative cell
Sample Tag folders	[sample_name]_Sample_Tag[number].zip [sample_name]_Multiplet_and_Undetermined.zip	Separate data tables and metric summary for cells assigned to each sample tag. Note: For putative cells that could not be assigned a specific Sample Tag, a Multiplet_and_Undetermined.zip file is also output.

Outputs when VDJ option selected:

Output	File	Content
VDJ metrics	[sample_name]_VDJ_Metrics.csv	Overall metrics from the VDJ analysis
VDJ per Cell	[sample_name]_VDJ_perCell.csv [sample_name]_VDJ_perCell_uncorrected.csv	Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type
VDJ Dominant Contigs	[sample_name]_VDJ_Dominant_Contigs_AIRR.csv	Dominant contig for each cell label chain type combination (putative cells only)
VDJ Unfiltered Contigs	[sample_name]_VDJ_Unfiltered_Contigs_AIRR.csv	All contigs that were assembled and annotated successfully (all cells)

Outputs for ATAC-Seq:

Output	File	Content
ATAC Metrics	[sample_name]_ATAC_Metrics.csv [sample_name]_ATAC_Metrics.json	Overall metrics from the ATAC-Seq analysis
ATAC Fragments	[sample_name]_ATAC_Fragments.bed.gz [sample_name]_ATAC_Fragments.bed.gz.tbi	Chromosomal location, cell index, and read support for each fragment detected
ATAC Transposase Sites	[sample_name]_ATAC_Transposase_Sites.bed.gz [sample_name]_ATAC_Transposase_Sites.bed.gz.tbi	Chromosomal location, cell index, and read support for each transposase site detected
ATAC Peaks	[sample_name]_ATAC_Peaks.bed.gz [sample_name]_ATAC_Peaks.bed.gz.tbi	Peak regions of transposase activity
ATAC Peak Annotation	[sample_name]_peak_annotation.tsv.gz	Estimated annotation of peak-to-gene connections
ATAC Datatables	[sample_name]_ATAC_Cell_by_Peak_MEX.zip	Peak regions of transposase activity per cell
ATAC Unfiltered Datatables	[sample_name]_ATAC_Cell_by_Peak_Unfiltered_MEX.zip	Unfiltered file containing all cell labels with >=1 transposase sites in peaks
ATAC BAM and BAM Index (if parameter is set)	[sample_name]_ATAC.bam [sample_name]_ATAC.bam.bai	Alignment file for R1 and R2 with associated I2 annotations for ATAC-Seq

Output when "Cell_Calling_Data: AbSeq" is selected:

Output	File	Content
Protein Aggregates Experimental	[sample_name]_Protein_Aggregates_Experimental.csv	Putative cell annotation showing cells suspected of resulting from protein aggregates