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cellranger-fgcz

Process 10x Genomics single-cell data with CellRanger on FGCZ SLURM infrastructure.

Updated May 28, 2026
Search Tags:#bioinformatics#single-cell#slurm#10x genomics#demultiplexing#cellranger#hto
One-click install
npx skills add https://github.com/cpanse/skills --skill cellranger-fgcz-cpanse
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cellranger-fgcz
Source: https://github.com/cpanse/skills/tree/main/single-cell-spatial-general/skills/cellranger-fgcz
Command: npx skills add https://github.com/cpanse/skills --skill cellranger-fgcz-cpanse

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve? Running CellRanger multi workflows for demultiplexing, VDJ, and feature barcoding is error-prone, especially when writing multi config CSV files, and many complex workflows like HTO+BCR without GEX are not supported by SUSHI and must be run manually on FGCZ infrastructure. ## Core Features & Use Cases - Multi Config Guidance: Create and validate CellRanger multi config CSVs for GEX+HTO, GEX+HTO+VDJ, OCM, CITE-seq, and multiome workflows with working example templates. - FGCZ-Specific Integration: Provides verified reference genome paths, storage conventions, g-req data management commands, and SLURM SBATCH job submission templates. - Validation Tools: Includes a Python script that checks config files and feature reference CSVs for format errors, invalid paths, duplicate barcodes, and wrong feature types before running CellRanger. - Use Case: You received a pooled 10x run with 4 HTO-tagged samples plus BCR libraries. Copy the example config, point it at your FASTQs and feature reference, validate it, and submit the SBATCH job to the cluster. ## Quick Start Ask the agent to create and validate a CellRanger multi config for a GEX plus HTO demultiplexing experiment in project p12345 and generate the SBATCH submission script.

Frequently Asked Questions about cellranger-fgcz

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I create a CellRanger multi config CSV for HTO demultiplexing?▼

Create a CSV with [gene-expression], [feature], [libraries], and [samples] sections, listing GEX and Multiplexing Capture FASTQs and mapping sample IDs to hashtag IDs. Copy the gex_hto example config and validate it with the included validate_config.py script before running.

How do I demultiplex on-chip multiplexing (OCM) samples with CellRanger?▼

Use cellranger multi with a [samples] section containing the ocm_barcode_ids column with values OB1 through OB4. No feature reference file is needed for OCM, unlike HTO demultiplexing.

What feature type should HTO barcodes use in CellRanger?▼

For Cell Ranger 6.0 and later, HTO barcodes must use the Multiplexing Capture feature type in the feature reference CSV. Using Antibody Capture for HTO demultiplexing is a common cause of failure.

Can CellRanger run VDJ and HTO without gene expression data?▼

Yes, a multi config with only [vdj], [feature], [libraries], and [samples] sections supports HTO plus BCR without GEX, with cell calling from VDJ reads. This workflow is not supported by SUSHI and must be run manually.

Why does CellRanger fail with FASTQ path not found at FGCZ?▼

CellRanger cannot access /srv/gstore/ directly from compute nodes. Copy FASTQs to /srv/GT/analysis/pXXXXX/ first, and confirm the fastq_id in the config matches the FASTQ filename prefix.

How do I submit a CellRanger job to the FGCZ SLURM cluster?▼

Copy the sbatch_cellranger.sh template, update the project ID, sample ID, and config path, create a logs directory, then run sbatch on the script. Monitor progress with squeue and the log files.

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