A rapid expression quantitative trait locus analysis approach using single cell or nucleus RNA sequencing (snRNAseq) of gametes from a small number of heterozygous individuals.
This repo contains snakemake pipelines, python scripts, and jupyter notebooks to reproduce the results of Parker et al., 2024, Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing.
This includes:
- Synteny analysis of parental genomes to identify high quality markers for genotyping and recombination analysis.
- Genotyping analysis and demultiplexing of cell barcodes that represent recombinant gametes originating from genetically different parental F1 hybrids.
- Spliced alignment of snRNAseq reads to both parental haplotypes simultaneously, using STAR diploid.
- A method for inferring recombination breakpoints and inherited haplotypes from sequenced markers for each gamete, using rigid hidden Markov models.
- Methods for performing eQTL analysis from inferred haplotypes and paired gene expression from each cell barcode.