Description

Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.

Input

Name (Type)
Description
Pattern

reference_name (string)

The name to give the new reference folder, e.g. my_vdj_ref. This flag is required

str

genes (file)

Reference transcriptome GTF file (optional)

*.gtf

fasta (file)

Reference genome FASTA file (optional)

*.{fasta,fa}

seqs (file)

Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional)

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

reference (directory)

Folder containing all the reference indices needed by Cell Ranger

versions (file)

File containing software version

versions.yml
included in
airrflow scrnaseq
maintainers
Github user ggabernet
Github user klkeys
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Tools

cellranger
10x Genomics EULA

Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser.

support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references