Description

Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command.

Input

Name (Type)
Description
Pattern

fasta (file)

Reference genome FASTA file

*.{fasta,fa}

gtf (file)

Reference transcriptome GTF file

*.gtf

motifs (file)

Sequence motif file (e.g., from transcription factors)

*.txt

reference_config (file)

JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path

config

reference_name (string)

The name to give the new reference folder

str

Output

Name (Type)
Description
Pattern

reference (directory)

Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc

versions (file)

File containing software version

versions.yml
included in
scrnaseq
maintainers
Github user ggabernet
Github user heylf
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

cellrangerarc
10x Genomics EULA

Cell Ranger Arc is a set of analysis pipelines that process Chromium Single Cell Arc data.

support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc