Mapping and Counting
Package Overview
Goal
Mapping of sequence data to reference genome
This analysis package is available for:
- Bulk RNA-seq and single-cell Smart-seq2 data (in-house pipelines)
- Bulk DNA-seq data (in-house pipelines)
- 10x single-cell RNA-seq data (Cell Ranger)
- 10x single-cell ATAC-seq data (Cell Ranger ATAC)
- 10x multiome data (Cell Ranger ARC)
- 10x Visium spatial data (Space Ranger)
- 10x Xenium spatial data (Xenium Ranger)
Requirements
- Reference sequence and gene annotation (for RNA-seq data) available in Ensembl or NCBI RefSeq
Analysis
- Running in-house and existing technology-specific pipelines
- Trimming of adapter and low quality bases, extracting UMI if applicable
- Mapping to a reference genome sequence
- Counting reads per gene and sample/cell (RNA-seq data)
- Quality control at different levels
Output
- Mappings in BAM format
- Gene counts as tables with gene annotations (RNA-seq data)
- MultiQC/HTML reports containing various QC metrics
- Other output from tech-specific pipelines
Advanced Analysis
- Include artificial constructs
- Setting up new tech-specific processing pipelines (only commercial technologies, limited support)