Single Cell ATAC-seq Quality Metric

Schema for submission of a scATAC-seq uniform pipeline quality metric.

Type

Lab specific identifiers to reference an object.

A lab specific identifier to reference an object.

Lab Alias

Aliases

The analysis step version of the quality metric.

Analysis Step Version

File Name

Image height

MD5sum

File size

MIME type

Image width

ATAC Bam Summary Stats

ATAC Fragment Summary Stats

ATAC Fragments Alignment Stats

Image Height

Hypertext REFerence

File Size

Image Width

Attachment

Award

Creation Timestamp

Description

Duplicate Number

Duplicate Fraction

Mitochondrial Fraction

Joint Barcodes Passing

Low Mapping Quality

Number of fragments mappig in multiple locations in the genome.

Multi-Mappings

Number Of Barcodes

Barcodes matching the expected list of valid barcodes.

Number Of Barcodes On Onlist

Potential mapping locations considered during alignment.

Number Of Candidates

Barcodes adjusted to match valid entries in the onlist.

Number Of Corrected Barcodes

Number Of Fragments

Reads successfully aligned to the reference genome.

Number Of Mapped Reads

Total successful alignments, including multiple mappings per read.

Number Of Mappings

Total alignments where reads map to multiple locations.

Number Of Multi-Mappings

Final count of fragments after deduplication and filtering.

Number Of Output Mappings

Total count of sequencing reads processed.

Number Of Reads

Reads aligned to multiple locations in the genome.

Number Of Reads With Multi-Mappings

Total alignments where reads map to a single location.

Number Of Uni-Mappings

Reads aligned to a single location in the genome.

Number Of Uniquely Mapped Reads

Notes

Percent Duplicates

The file(s) to which this quality metric applies.

Quality Metric Of

Release Timestamp

The version of the JSON schema that the server uses to validate the object.

Schema Version

Status

Submitted By

Additional information specified by the submitter to be displayed as a comment on the portal.

Single Cell ATAC-seq Quality Metric

Changelog for `single_cell_atac_seq_quality_metric.json`

Minor changes since schema version 1

Single Cell ATAC-seq Quality Metric

Changelog for single_cell_atac_seq_quality_metric.json

Minor changes since schema version 1

Changelog for `single_cell_atac_seq_quality_metric.json`