Cell Ranger (v7.0.0) is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Steps:
- Cellranger count takes FASTQ files performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis. cellranger count also processes Feature Barcoding data alongside Gene Expression reads.
- Cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data. The aggr pipeline can be used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis.
Please check following web site for detailed information: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Inputs:
- Reads
- Mate (single or pair)
Citation:
If you use DolphinNext in your research, please cite: Yukselen, O., Turkyilmaz, O., Ozturk, A.R. et al. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020). https://doi.org/10.1186/s12864-020-6714-x
Program Versions:
- Cellranger-v7.0.0
- fastqc=0.11.8
- multiqc=1.7
- Cellranger-atac-2.0.0.
- bcl2fastq2=2.20.0.422
- samtools=1.3
- igvtools=2.5.3
- bedtools=2.30.0
Containers:
- Docker: dolphinnext/cellranger:6.0
- Singularity: https://galaxyweb.umassmed.edu/pub/dolphinnext_singularity/UMMS-Biocore-singularity-cellranger-v6.simg