Description

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

Input

Name
Description
Pattern

fasta (file)

Reference genome FASTA file

*.{fasta,fa}

gtf (file)

Reference transcriptome GTF file

*.gtf

motifs (file)

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

*.txt

reference_config (file)

JSON-like config 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
Description
Pattern

0 ()

0 ()

Tools

cellranger-atac Documentation

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

License: 10x Genomics EULA
Authors