Published February 9, 2022 | Version 1.0
Dataset Open

10 scRNA-seq datasets processed using 3 unspliced counting pipelines

  • 1. ROR icon California Institute of Technology

Description

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 https://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.

Other

Related Publication: RNA velocity unraveled Gennady Gorin Caltech Meichen Fang Caltech Tara Chari Caltech Lior Pachter Caltech bioRxiv eng

Files

Files (2.3 GB)
Name Size
md5:0f747ddda62f72cd035df381ffc1f8ae
780.3 MB Download
md5:405ae30f0dcaa1b02cf41a1a1ca128b0
44.1 MB Download
md5:fcf8c22bf26c2c824ff88052e01816e3
48.0 MB Download
md5:bbd853401e492db25e5112cd11eb29a0
719.3 MB Download
md5:2a00f736d24a438b9de4be391d774d48
677.3 MB Download

Additional details

Created:
September 8, 2022
Modified:
November 18, 2022