ScaleRna Outputs Overview

Analysis workflow results for all samples in the run will appear in the output directory defined by --outDir (ScaleRna.out by default). The pipeline generates outputs organized into specialized directories, each containing detailed results and quality metrics.

Output Directory Structure

ScaleRna.out/
├── alignment/          # STAR and STARSolo alignment results
├── barcodes/           # Barcode demultiplexing and metrics
├── fastq/              # FASTQ generation and quality control
├── reports/            # QC reports and summary statistics
├── samples/            # Processed gene expression matrices
└── scaleplex/          # ScalePlex-specific outputs (if applicable)

Detailed Output Documentation

Each output directory contains specialized results and is documented in detail:

Samples Output - Processed gene expression matrices, cell metrics, and analysis-ready data
Alignment Output - Raw STAR alignment results, gene expression matrices, and alignment statistics
QC Reports - Comprehensive quality control reports and summary statistics
Barcodes Output - Barcode demultiplexing results, error rates, and quality metrics
Fastq Output - FASTQ quality control reports, file assignments, and sequencing metrics

Key output files

Directory	File	Description
`reports`	`multiqc_report.html`	MultiQC report for fastq generation, fastQC and trimming
	`<sample>.<libIndex2>.report.html`	A standalone report including key QC metrics and figures for each sample; (`merged` for extended throughput runs)
	`<sample>_libraries`	For QuantumScale runs, individual sample reports for each library separately
	`allSamples.reportStatistics.csv`	QC metrics from all samples in this analysis in one table
	`reads_per_sample.csv`	Number of passing reads per sample post barcode demux
	`csv/`	Summary and QC metrics for this sample in csv format
`reports/library`	`library_<libIndex2>.report.html`	Barcode summary and demultiplexing statistics for the whole sequencing library
	`csv/`	Summary and QC metrics for this library in csv format
`samples`	`<sample>.<libIndex2>.filtered.matrix/`	Pre-filtered gene expression matrix for passing cells; `merged` for results combined across multiple libraries
	`<sample>.<libIndex2>.allCells.csv`	Metrics per called cell, including barcodes / well positions
	`<sample>_libraries/`	For QuantumScale runs, this contains output files per libIndex2
`fastq`	`fastqc/*_fastqc.html`	fastqc report for each fastq file in the sequencing library
	`Reports/`	Fastq generation summary reports from bcl-convert
`barcodes`	`split_bcparser_jobs/bcparser.<libIndex2>/<sample>.bam`	Sample unaligned bam files (Demultiplexed and barcode error-corrected); only included with `--bamOut true`
	`<libIndex2>.metrics.json`	Detailed barcode and demultiplexing information, including individual barcode error rates
`alignment/<sample>.<libIndex2>`	`<sample>.star.align/`	STAR alignment output, including BAM file, with single-cell barcode and UMI information in tags
	`<sample>.star.solo/`	STARSolo output for each sample, including unfiltered `.mtx` files

Need Help?

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