This repository contains all code to reproduce the results from our ASE-spermatogenesis paper.
All data is available at ArrayExpress under the accession number E-MTAB-6934 (previously published B6 samples, https://www.nature.com/articles/s41467-019-09182-1) and E-MTAB-11602 (everything else). This includes raw read files, total and allele-specific quantifications as well as filtered count matrices with cell type annotations. The ATAC-Seq data is deposited under the accession number E-MTAB-12685.
Scripts to perform allele-specific expression quantifications can be found in /Analysis/Alignments/scRNASeq/. For standard processing of 10x single-cell RNA-Sequencing data, CellRanger was used with default settings. Further preprocessing scripts can be found in /Analysis/. A snakemake workflow to process the ATAC-Seq data can be found in /Analysis/Alignments/ATACSeq/.
All analysis scripts can be found in /Analysis/, including the figures they mainly refer to as well as scripts to reproduce all plots in the figures.
Jasper Panten ([email protected])