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Quantify gene expression in a single cell RNA-seq dataset.

module

Inputs

Channel nameDescriptionType
optMap of task-specific variables.map
tagUnique identifier to use in the tag directive.string
idDirectory-safe name for the output directory.string
descriptionA short description of the sample.string
sampleName of sample used in FastQ file name.string
fastq_path_?List of directories in which the FastQ files can be found. The symlinks to the paths will be incrementally numbered from 1 at the ? placeholder.paths
index_pathPath to the properly-formatted index directory.path

Outputs

Emission nameDescriptionTypeFilename pattern
optMap of task-specific variables.map
taskYAML-formatted file of task parameters and software versions used by the task.filetask.yaml
quantification_pathCell Ranger outputs (outs/) directory.path<id>/outs
cell_ranger_reportHTML summary report.file

Tools

cell ranger extcount multithreaded

Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

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