modules/
cellranger_vdj

Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.

align vdj reference immunoprofiling single-cell cellranger

https://github.com/nf-core/modules/tree/master/modules/nf-core/cellranger/vdj

Description

Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.

Input

Name

Description

Pattern

`0` ()

`1` ()

`reference` (directory)

Folder containing all the reference indices needed by Cell Ranger

Output

Name

Description

Pattern

`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