Description

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

Input

Name
Description
Pattern

fasta (file)

Reference genome FASTA file (optional)

*.{fasta,fa}

gtf (file)

Reference genome GTF file (optional)

*.gtf

seqs (file)

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

*.{fasta,fa}

reference_name (string)

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

str

Output

Name
Description
Pattern

0 ()

0 ()

Tools

cellranger Documentation

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.

License: 10x Genomics EULA
Authors