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)