count
Quantify gene expression in a single cell RNA-seq dataset.
moduleInputs
| Channel name | Description | Type |
|---|---|---|
opt | Map of task-specific variables. | map |
tag | Unique identifier to use in the tag directive. | string |
id | Directory-safe name for the output directory. | string |
description | A short description of the sample. | string |
sample | Name 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_path | Path to the properly-formatted index directory. | path |
Outputs
| Emission name | Description | Type | Filename pattern |
|---|---|---|---|
opt | Map of task-specific variables. | map | |
task | YAML-formatted file of task parameters and software versions used by the task. | file | task.yaml |
quantification_path | Cell Ranger outputs (outs/) directory. | path | <id>/outs |
cell_ranger_report | HTML 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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