Software Open Access

BICF Cellranger count Analysis Workflow

Gervaise H. Henry; Jeremy A. Mathews; Jonathan R. Gesell; Venkat S. Malladi

Project member(s)
Holly Ruess

BICF Cellranger count Analysis Workflow is a wrapper for the CellRanger count tool from 10x Genomics. It was developed by BICF and Strand Lab and used by the BICF at UT Southwestern Dept. of Bioinformatics.

The pipeline uses Nextflow a bioinformatics workflow tool. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.

This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.

Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.

Pipeline is maintained at Git repository.

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