Analysis workflow results for all samples in the run will appear in the output directory defined by --outDir (ScaleRna.out by default).
For detailed information about the library and sample level QC reports see qcReport.md
| 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 --bcParserBamOut 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 |
The gene expression matrix directories (.mtx) can be loaded into Seurat, ScanPy or similar tools for visualization or downstream analysis.
Columns in the <sample>.<libIndex2>.allCells.csv file:
| Column name | Description |
|---|---|
| cell_id | Unique id for cell composed of barcodes detected |
| counts | The number of unique transcript molecules detected |
| genes | The number of unique genes detected |
| totalReads | The number of reads demultiplexed to this cell barcode |
| countedReads | The number of reads contributing to counts in the expression matrix |
| mappedReads | The number of reads that aligned to the genome |
| geneReads | The number of reads that mapped to an annotated gene |
| exonReads | The number of reads that mapped to an exon |
| intronReads | The number of reads that mapped to an intron |
| antisenseReads | The number of reads mapping antisense to annotated exons |
| mitoReads | The number of reads mapping on mitochondrial genome |
| countedMultiGeneReads | The number of multi-gene reads that contributed to counts in the expression matrix |
| Saturation | 1 - (UniqueReads / TotalReads) on Reads Mapped to Transcriptome |
| mitoProp | Proportion of mapped reads that aligned to mitochondrial genome |
| PCR | The alias for the PCR (library) barcode |
| RT | RT plate well |
| bead_bc | The bead barcode (microwell) |
| sample | The sample name |
| flags | QC flags |