/BenchmarkAlignment

Primary LanguageShellMIT LicenseMIT

Comparative Analysis of common alignment tools for single cell RNA sequencing

This repository contains all the scripts that where used in the folowing paper:

Bruening et.al. - Comparative Analysis of common alignment tools for single cell RNA sequencing" - Gigascience 2021 [Under Revision]

The repository contains two main folders. The "mapping" folder contains all the scripts and files that are required for the alignment procosees. The "references" folder contains the script to download the reference genomes for mouse and human and to generate the mapping indices.

Detailed remarks for the individual files can be found in the ReadMe.md withing the respective folders

Description of Files

  • mapping folder All required scripts for the Alignments
  • reference folder Scripts to download reference genome and create alignment indices
  • make_figures.rmd creates the figures that are included in the paper.