/
output_definition.json
156 lines (156 loc) · 6.1 KB
/
output_definition.json
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{
"files": {
"workflow-report": {
"filepath": "./wf-single-cell-report.html",
"title": "workflow report",
"description": "Report for all samples",
"mime-type": "text/html",
"optional": false,
"type": "aggregated"
},
"sample-data": {
"filepath": "./fastq_ingress_results/reads/{{ alias }}.fastq.gz",
"title": "Concatenated sequence data",
"description": "Per sample reads concatenated in a single FASTQ file.",
"mime-type": "text/json",
"optional": false,
"type": "per-sample"
},
"results-summary": {
"filepath": "./{{ alias }}/{{ alias }}.config_stats.json",
"title": "Results summaries",
"description": "Results summaries including adapter configuration numbers.",
"mime-type": "application/json",
"optional": false,
"type": "per-sample"
},
"gene-expression": {
"filepath": "./{{ alias }}/{{ alias }}.gene_expression.counts.tsv",
"title": "Gene expression counts",
"description": "Gene x cell expression matrix.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"gene-expression-processed": {
"filepath": "./{{ alias }}/{{ alias }}.gene_expression.processed.tsv",
"title": "Processed gene expression counts",
"description": "Filtered and normalized gene x cell expression matrix.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"transcript-expression": {
"filepath": "./{{ alias }}/{{ alias }}.transcript_expression.counts.tsv",
"title": "Transcript expression counts",
"description": "Transcript x cell expression matrix.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"transcript-expression-processed": {
"filepath": "./{{ alias }}/{{ alias }}.transcript_expression.processed.tsv",
"title": "Processed transcript expression counts",
"description": "Filtered and normalized transcript x cell expression matrix.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"mitochondrial-expression": {
"filepath": "./{{ alias }}/{{ alias }}.gene_expression.mito.tsv",
"title": "Mitochondrial expression levels",
"description": "Per cell mitochondrial gene expression as percentage total of total gene expression.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"knee-plot": {
"filepath": "./{{ alias }}/{{ alias }}.kneeplot.png",
"title": "Knee plot",
"description": "Knee plot illustrating the filtering of cells by read count.",
"mime-type": "image/png",
"optional": false,
"type": "per-sample"
},
"saturation-curves": {
"filepath": "./{{ alias }}/{{ alias }}.saturation_curves.png",
"title": "Saturation curves",
"description": "Saturation plots that indicate sampling of library complexity.",
"mime-type": "image/png",
"optional": false,
"type": "per-sample"
},
"read-tags": {
"filepath": "./{{ alias }}/{{ alias }}.read_tags.tsv",
"title": "Read tags",
"description": "Per read assigned barcodes UMIs genes and transcripts.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"barcode-counts": {
"filepath": "./{{ alias }}/{{ alias }}.uncorrected_bc_counts.tsv",
"title": "Barcode counts",
"description": "The counts of each barcode present in the sequenced library (only barcodes that have a 100% match in the 10x whitelist are included).",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"whitelist": {
"filepath": "./{{ alias }}/{{ alias }}.whitelist.tsv",
"title": "Whitelist",
"description": "The barcodes found in the library that remain after filtering.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"alignment-per-chromosome": {
"filepath": "./{{ alias }}/bams/{{ alias }}.{{ chromosome }}.tagged.bam",
"title": "Alignment output per chromosome",
"description": "Genomic alignment output file per chromosome.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-index-per-chromosome": {
"filepath": "./{{ alias }}/bams/{{ alias }}.{{ chromosome }}.tagged.bam.bai",
"title": "Alignment index per chromosome",
"description": "Genomic alignment index file per chromosome.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-per-sample": {
"filepath": "./{{ alias }}/bams/{{ alias }}.tagged.sorted.bam",
"title": "Alignment output per sample",
"description": "Genomic alignment output file with aggregated chromosomes (when using --merge_bam).",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-index-per-sample": {
"filepath": "./{{ alias }}/bams/{{ alias }}.tagged.sorted.bam.bai",
"title": "Alignment index per sample",
"description": "Genomic alignment index file with aggregated chromosomes (when using --merge_bam).",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"transcriptome_fasta": {
"filepath": "./{{ alias }}/{{ alias }}.transcriptome.fa.gz",
"title": "Transcriptome sequence",
"description": "Transcriptome generated by Stringtie during transcript discovery stage",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcriptome_annotation": {
"filepath": "./{{ alias }}/{{ alias }}.transcriptome.gff.gz",
"title": "Transcriptome annotation",
"description": "Transcriptome annotation generated by Stringtie during transcript discovery stage",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
}
}
}