p4rkerw / salsa

Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

Welcome to 🌶️SALSA! Single Cell Allele Specific Analysis

Here you will find a workflow to analyze single cell allele-specific expression and chromatin accessibility obtained from 10X Genomics Single Cell Gene Expression and Single Cell ATAC datasets. To get started follow along with one of our tutorials.

If you use 🌶️SALSA please cite the following manuscript

Wilson PC, Muto Y, Wu H, Karihaloo A, Waikar SS, Humphreys BD.
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
Nat Commun 13, 5253 (2022). 
https://doi.org/10.1038/s41467-022-32972-z
PMID: 36068241

Thanks!
Parker

Visit the Wilson lab website:
www.parkerwilsonlab.com

Visit the Humphreys lab website:
www.humphreyslab.com

Check out our interactive datasets with Kidney Interactive mulTiomics (KIT):
http://humphreyslab.com/SingleCell/

Find us on Twitter:
@parkercwilson @HumphreysLab

Find us on Docker Hub:
p4rkerw@dockerhub

salsa's Issues

Determining Allele-Specific Expression (ASE) using SALSA

Hello,
Thank you for developing this nice tool.
I have single-cell RNA sequencing (scRNA-seq) data from tissues generated by crossing two distinct mouse strains. I am aware of the single nucleotide variants (SNVs) in the parent genomes. I am interested in determining Allele-Specific Expression (ASE) in all expressed genes within my offspring scRNA-seq dataset. What is the best approach for conducting this analysis using SALSA tool? Do you have a pipeline designed for this purpose?

Thank you