This repo includes the analysis used in the manuscript "Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments"
In this analysis we re-processed raw data from Yao et al 2021 and Thrupp et al 2020 to obtain UMI counts with and without introns.
Raw data were acquired from: Yao et al nuclei: https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/10x_v3/mouse/raw/MOp/
Yao et al cells: https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v3/mouse/raw/MOp/
Thrupp et al: GEO accessions GSE153807 and GSE137444
Includes main statistical analysis and plotting for the figures
Shows how STARsolo outputs were imported and collated
Confirms that STARsolo output matches the original CellRanger output from Yao et al.