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External Data Sources

Source: vignettes/data-sources.Rmd
data-sources.Rmd

Data files for FastQDesign are hosted on Zenodo for reproducibility and easy access. Note: Some large data files (like BAM files and RDS objects) are not included in the R package due to size limits.

BAM Files (scRNA-seq alignments)

Download from: https://zenodo.org/records/19073177

Contains Cellranger-aligned BAM files with cell barcodes (CB tag) and UMI (UB tag):

File Size
P1_AI_possorted_genome_bam.bam 13.1 GB
P1_AI_possorted_genome_bam.bam.bai 4.1 MB
P1_BM_possorted_genome_bam.bam 14.4 GB
P1_BM_possorted_genome_bam.bam.bai 4.4 MB

Reference Data and Power Analysis

Download from: https://zenodo.org/records/19072084

Contains pre-processed Seurat objects and power analysis data:

File Description Size
reference_list.rds Reference SamplePrep output 191.2 MB
bam_downsample_list.rds Processed downsampled data 77.9 MB
AIBM_power.csv Power analysis data for experiment design ~6 KB

URL Streaming (No Download Required)

BAM files can be accessed directly from Zenodo URL without downloading.

Using Rsamtools 

library(Rsamtools)

bam_url <- "https://zenodo.org/records/19073177/files/P1_AI_possorted_genome_bam.bam"
bai_url <- "https://zenodo.org/records/19073177/files/P1_AI_possorted_genome_bam.bam.bai"

bf <- BamFile(bam_url, index = bai_url)
header <- scanBamHeader(bf)

Using fastF

fastF supports URL streaming for extract and crb subcommands:

# Extract CR tags (UMI sequences)
# Processes 182M reads in ~8 minutes from URL
FastQDesign::fastF_extract(
  bam = "https://zenodo.org/records/19073177/files/P1_AI_possorted_genome_bam.bam",
  tag = "CR",
  type = 0
)

The extract subcommand streams BAM via htslib’s HTTP support. For very large files, this is efficient as only necessary regions are downloaded.

Local Download 

# Download BAM
download.file(
  "https://zenodo.org/records/19073177/files/P1_AI_possorted_genome_bam.bam",
  destfile = "P1_AI_possorted_genome_bam.bam"
)

# Download Seurat object
download.file(
  "https://zenodo.org/records/19072084/files/reference_list.rds",
  destfile = "reference_list.rds"
)

library(Seurat)
seurat_obj <- readRDS("reference_list.rds")

Citation 

Wang Y (2026). FastQDesign Test Data. Zenodo.
https://zenodo.org/records/19072084
https://zenodo.org/records/19073177