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Single Cell RNA-seq Quality Metric

Schema Directory
Title
Single Cell RNA-seq Quality Metric
Description
Schema for submission of a scRNA-seq uniform pipeline quality metric.
Version
v2
Required
analysis_step_version, award, lab, quality_metric_of
Identifying Properties
aliases, uuid
Highlight properties with matching names, “title” attributes, or an enum of those properties. Matching properties might be non-submittable.
array[string]
Lab specific identifiers to reference an object.
linkto
The analysis step version of the quality metric.
object
The attached content.
linkto
Grant associated with the submission.
string
A plain text description of the object.
number
Number of BUS records for Good-Toulmin estimation.
number
Version of Kallisto index command used for building the transcriptome index.
number
Length of k-mers used for building the transcriptome index.
linkto
Lab associated with the submission.
number
Mean number of reads per cell barcode.
number
Mean number of UMIs per cell barcode.
number
Median number of reads per cell barcode.
number
Median number of UMIs per cell barcode.
number
Total number of UMIs associated with cell barcodes.
number
Total number of valid cell barcodes detected.
number
Number of bootstrap iterations used to estimate expression uncertainty.
number
Number of valid reads processed by Kallisto.
number
Number of reads that could be pseudoaligned to the transcriptome index.
number
Total number of input reads.
number
Number of records in BUS file.
number
Total number of target sequences (e.g., transcripts) in the index.
number
Number of reads that could be pseudoaligned to a unique target sequence.
number
Number of cell barcodes matching an expected list of barcodes (onlist).
number
Number of reads associated with barcodes on the onlist.
number
Percentage of reads that could be pseudoaligned to the transcriptome index.
number
Percentage of reads that could be pseudoaligned to a unique target sequence.
number
Percentage of cell barcodes matching an expected list of barcodes (onlist).
number
Percentage of reads associated with barcodes on the onlist.
array[linkto]
The file(s) to which this quality metric applies.
object
The content of the kb-python RNAseq kb_info.json file.
string
Additional information specified by the submitter to be displayed as a comment on the portal.
number
Total number of UMIs detected.