Species Mixing

Below are the files needed for the species mixing experiment

• 10xv3 Whitelist Barcodes
• Transcripts to Genes map for Humans and Mouse

Count data for tutorial `Aggregating multiple count matrices`

E-MTAB-6108_sample1_sample2_genecounts.zip
├── sample1
│   ├── genecounts
│   │   ├── genes.barcodes.txt
│   │   ├── genes.genes.txt
│   │   └── genes.mtx
│   ├── matrix.ec
│   ├── run_info.json
│   └── transcripts.txt
└── sample2
    ├── genecounts
    │   ├── genes.barcodes.txt
    │   ├── genes.genes.txt
    │   └── genes.mtx
    ├── matrix.ec
    ├── run_info.json
    └── transcripts.txt

Files for Velocity Tutorial (human)

This page provides the files needed to follow the velocity started tutorial. The experiment is single-cell RNA-sequencing of human week 10 fetal forebrain dataset (SRR6470906 & SRR6470907) from this paper (https://doi.org/10.1038/s41586-018-0414-6).

Below are the:

cDNA Transcripts FASTA cDNA.correct_header.fa.gz
cDNA Transcripts list cDNA_transcripts.to_capture.txt.gz

Intron Transcripts FASTA introns.correct_header.fa.gz
Intron Transcripts list introns_transcripts.to_capture.txt.gz

cDNA Intron Transcripts to Genes map cDNA_introns.t2g.txt.gz

10x Chromium v2 chemistry barcode whitelist 10xv2_whitelist.txt

Files for Getting Started

This page provides the files needed to follow the getting started tutorial. The experiment is single-cell RNA-sequencing of mouse retinal cells SRR8599150 from this paper (https://doi.org/10.1016/j.immuni.2019.02.007).

Below are the:

• Mouse transcriptome Mus_musculus.GRCm38.cdna.all.fa.gz
• 10x Chromium v2 chemistry barcode whitelist 10xv2_whitelist.txt
• Mouse transcripts to genes map transcripts_to_genes.txt
• Read 1 fastq file SRR8599150_S1_L001_R1_001.fastq.gz
• Read 2 fastq file SRR8599150_S1_L001_R2_001.fastq.gz
• Expected files (corrected sorted BUS file, transcripts file, equivalence class file) output.correct.sort.bus.gz transcripts.txt.gz matrix.ec.gz
• (extended explanation) Transcripts to genes utility t2g.py