mkref

Creates an index for use with Cell Ranger ARC. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.

module

Inputs

Channel nameDescriptionType
optA map of task-specific variables.map
tagAn identifier to use in the tag directive.string
organismName of the organism (eg. Mus_musculus)string
assemblyGenome assembly (eg. mm10)string
mon-nuclear contigsAn array of chromosome names present in the FastA and GTF files that are not in the nucleus and therefore lack chromatin structure.strings
motifsPath to the transcription factor motifs in JASPAR format.file
path to FastAsPath to directory containing FastA files to index. These will be concatenated into a single FastA file.path
path to GTFsPath to directory containing GTF files. These will be concatenated into a single GTF file.path

Outputs

Emission nameDescriptionTypeFilename pattern
optA map of task-specific variables.map
taskYAML-formatted file of task parameters and software versions used by the task.filetask.yaml
pathPath to the newly created index.path

Tools

cell ranger arc multithreaded

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage. Furthermore, since the ATAC and GEX measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and GEX.

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