Assays Table

Field

Used for 10X Genomics

Used for non-10X Genomics

Used for Custom Matrices

Required

sample

no

no

yes

yes

replicate

no

no

yes

optional

assay.name

no

no

yes

optional

path

no

no

yes

optional

Note

  • Assay table is only used if you have calculated custom feature-by-barcode counts matrices. For example, if one has a genome annotation file containing gene coordinates and enhancer coordinates, you can count all ATAC reads mapping to a gene and associated enhancers:

    Gene Activity Score = reads mapped within gene + reads mapped to enhancers.

  • Do not use this table for calculating standard Gene Activity Scores (GAS) common to ATAC analyses. This is included in the standard ATAC Peaks workflow. For details about the standard GAS included in this workflow, see Signac Documentation.

Field descriptions

sample

string. Defines labels for each sample. Values in sample column must be unique, unless analyzing technical replicates. If specifying technical replicates, sample label must be the same for all rows containing techical replicates.

replicate

string. Optional. Defines labels for each technical replicate of a sample. Values in replicate column must be unique per sample. If not specified technical replicates, leave empty. If specified technical replicates: sample must be the same for all rows containing techical replicates.

assay.name

string. Optional. Name of custom feature-by-barcode counts matrix. If not specified Leave empty. If specified Name of custom feature-by-barcode counts matrix (string). Cannot be Gene.Expression, Peaks, or TF.

path

string. Optional. Path to custom feature-by-barcode counts matrix. If not specified Leave empty. If specified Path to custom feature-by-barcode counts matrix in HDF5 or RDS format, or path to parent directory of MEX formatted matrix, barcode and features files.

Example

A basic example of an assays.tsv file is below. This table represents an experiment where a custom enhancer counts matrix was calculated in addition to ‘core’ cellranger analyses.

sample

replicate

assay.name

path

pbmc1

ipsc

enhancer

pbmc1/assays/enhancer_bc_matrix.h5

See Overview of workflows for more detailed examples of config files.