outputs.md

Outputs

Analysis workflow results for all samples in the run will appear in the output directory defined by --outDir (out by default).

Path	File	Description
<sample>.report.html	<sample>.report.html	An interactive standalone HTML report including key metrics/figures for each sample
fastq	<fastqName>.fastq.gz	Fastqs derived from specified runFolder doesn't exist if fastqDir passed instead.
fastq/fastqc/	<fastqName>_fastqc.html	A fastqc generated HTML report for the given fastq
demux/<fastqName>.demux	<sample>.fastq.gz	Demultiplexed fastq files
	metrics.json	Read aligning and Barcode matching statistics for Samples within fastqName. Barcode statistics separated into: - droplet (drop) - index - tagmentation (tgmt)
align	<sample>.fragments.tsv.gz	Fragments file generated for <sample>
	<sample>.bam	Alignment of reads derived from <sample> to genome specified in experiment.config
align/dedup	<sample>.dedup_stats.tsv	Table denoting proportion of Passing, Unique and Mitchondrial reads between all cells in <sample>
	<sample>.cell_stats.tsv	Table containing number of Passing, Unique and Mitochondrial reads per barcode.
peaks	<sample>_peaks.narrowPeak	macs3 called peaks for <sample> in narrowPeak format
peaks/<sample>.counts	features.tsv matrix.mtx metrics.tsv	Components of a Cell by Peak count matrix in MEX format for <sample>
	metrics.tsv	Table denoting: - unique barcodes counted - unique features counted - reads counted - fraction of total reads ? Fraction reads counts? included in peaks
	barcodes.stats.tsv	Table denoting: - number of unique peaks - total counts - Fraction of reads in peaks per barcode
peaks/<sample>.tss_counts	features.tsv matrix.mtx metrics.tsv	Components of a Cell by Gene count matrix (based on reads mapping to peaks in TSS regions). MEX format for <sample>
	metrics.tsv	Table denoting: - unique barcodes counted - unique features counted - reads counted - fraction of total reads ? Fraction reads counts? included in peaks at TSS
	barcodes.stats.tsv	Table denoting: - number of unique peaks in TSS regions - total counts - Fraction of reads in peaks at TSS regions per barcode
QC/<sample>	thresholds.json	JSON containing thresholds for minimum read counts (ReadsThresh) and minimum reads in peaks counts (ReadsInPeaksThresh) derived from passed QC Filtering Params
	QC.tsv	Table denoting which cells are to be included in downstream analysis (Pass) as well as the qc filtering criteria they failed if any (Filter)
ArchR/<sample>*	Save-ArchR-Project.rds	R data structure used to reopen automated analysis in ArchR. Dependent on: - ArrowFiles - Embeddings - ImputeWeights - IterativeLSI Existing in the same folder to successfully instantiate.
	geneScore	Components of a Cell by Gene Score matrix in MEX format . How ArchR calculates gene scores from ATAC data
	Plots	PDF files with figures of: - TileMatrix based UMAP - Heatmap of marker genes (by genescore) for all clusters - UMAP embeddings colored by top 10 marker genes for each cluster **
	Top10Markers.tsv	Table denoting (at most) top 10 marker genes (by gene score) for each derived **cluster

• *ArchR output is only generated if json specified as the genome field in params contains either:

  • To use builtin annotations: An archrAlias
    * Must also specify: params.useBuiltInGenome = true in experiment.config
  • To use custom annotations: A name of a BSGenome (as BSGenome), a gtf and an annotationConvention

• **Output related to marker genes is only generated if getMarkerGenes is set to true in your qcAndArchRParams yml. Use this documentation to modify parameters in this yml.