Using fastF Tool • FastQDesign

The fastF tool is a C-based command-line utility for scRNA-seq experiment design. It provides several subcommands for processing FastQ and BAM files.

Installation

The fastF binary is automatically installed with the FastQDesign package:

devtools::install_github("yuw444/FastQDesign")

Package Test Data

The package includes small test files for learning the fastF workflow:

# Paths to package test data (small files)
test_R1 <- system.file("data", "test_R1.fastq.gz", package = "FastQDesign")
test_R2 <- system.file("data", "test_R2.fastq.gz", package = "FastQDesign")
test_bam <- system.file("data", "test.bam", package = "FastQDesign")
test_features <- system.file("data", "features.tsv.gz", package = "FastQDesign")
test_barcodes <- system.file("data", "barcodes.tsv.gz", package = "FastQDesign")
test_whitelist <- system.file("data", "whitelist.txt", package = "FastQDesign")

fastF Subcommands

1. Find Cell Barcode Whitelist

Extract cell barcode whitelist from FastQ files:

# Find whitelist from R1 FastQ file
FastQDesign::fastF_freq(
  R1 = test_R1,
  out = "output_dir",
  len = 16L
)

This creates whitelist.txt in the output directory.

2. Filter FastQ Files

Filter FastQ files using a whitelist and downsampling:

FastQDesign::fastF_filter(
  R1 = test_R1,
  R2 = test_R2,
  whitelist = test_whitelist,
  out = "filtered_dir",
  len = 16L,
  seed = 42L,
  rate = 0.1
)

3. Extract CR/CB Tags from BAM

Summarize cell barcode and UMI information:

FastQDesign::fastF_crb(
  bam = test_bam,
  out = "output.tsv.gz"
)

4. Convert BAM to Matrix

Convert BAM to sparse matrix format:

FastQDesign::fastF_bam2db(
  bam = test_bam,
  feature = test_features,
  barcode = test_barcodes,
  out = "matrix_dir"
)

5. Extract Custom Tags

Extract custom tags from BAM files:

FastQDesign::fastF_extract(
  bam = test_bam,
  tag = "CB"
)

Running from Command Line

You can also run fastF directly from the command line:

# Find whitelist
fastF freq -R input_R1.fastq.gz -l 16 -o output_dir/

# Filter FastQ
fastF filter -R input_R1.fastq.gz -r input_R2.fastq.gz -w whitelist.txt -o filtered/

# Extract CR/CB tags
fastF crb -b input.bam -o output.tsv.gz