10 scRNA-seq datasets processed using 3 unspliced counting pipelines

This dataset contains ten 10X scRNA-seq datasets (two v2 from Desai et al., DOI: 10.1126/science.abc6506, eight v3 generated by 10X Genomics) that have been processed using pipelines for spliced and unspliced molecule quantification. We used velocyto, kallisto|bustools (kb), and salmon/alevin-fry to process the raw FASTQ files, and output loompy files with spliced and unspliced count matrices. The scripts used for processing, as well as the notebook used for post-processing, visualization, and comparisons are available at github.com/pachterlab/gfcp_2022.

The following files are included. raw_loom_sm.tar.gz: all salmon outputs. raw_loom_10x_kb.tar.gz: kb outputs for 10X data. raw_loom_10x_vc.tar.gz: velocyto outputs for 10X data. raw_loom_desai_kb.tar.gz: kb outputs for Desai data. raw_loom_desai_vc.tar.gz: velocyto outputs for Desai data.