10X Genomics Pipeline
10X Genomics is the company that pioneered scRNA-seq.
The Chromium platform is used for sequencing individual cells. The resulting data is then processed using the Cell Ranger pipeline.
Cell Ranger Pipeline:
- Reads are first aligned to a reference genome.
- Next, low-quality reads are filtered out.
- Barcodes are then counted to identify individual cells.
- UMIs (unique molecular identifiers) are counted to quantify transcripts.
- Finally, expression matrices are generated for downstream analysis.
UVA RC has Cell Ranger on Rivanna, so you can use it to process your scRNAseq data. This tutorial will not go into details about that, instead focusing on visualization/downstream analysis.
10X Genomics Cell Ranger Outputs
barcodes.tsv
This file lists 1 barcode per cell.
genes.tsv
This file contains the Ensembl IDs and gene symbols.
matrix.mtx
This file contains the actual expression data.
