Prepare Short-Read Data for Quantification — mpaqt_prepare_short

Process short-read data from various input types for MPAQT quantification. Supports three input pathways:

mpaqt_prepare_short_reads(
  index,
  fastq_1 = NULL,
  fastq_2 = NULL,
  bus_file = NULL,
  ec_file = NULL,
  rds_file = NULL,
  output_file = NULL,
  keep_bus = FALSE,
  output_dir = tempdir(),
  threads = 1L,
  verbose = TRUE
)

Arguments

index: An mpaqt_index object (bundled or with valid kallisto_index path)
fastq_1: Path to first FASTQ file (R1) for paired-end reads
fastq_2: Path to second FASTQ file (R2) for paired-end reads
bus_file: Path to pre-computed BUS file (from kallisto bus)
ec_file: Path to EC mapping file (matrix.ec from kallisto bus)
rds_file: Path to pre-computed mpaqt_counts_sr RDS file
output_file: Path to save the final RDS file (default: output_dir/mpaqt.short_read.rds)
keep_bus: Keep intermediate kallisto/bustools files (default: FALSE).
output_dir: Output directory for results (default: tempdir())
threads: Number of threads for kallisto (default: 1)
verbose: Print progress messages (default: TRUE)

Value

An mpaqt_counts_sr object (invisibly)

Details

Raw FASTQ files: Run kallisto bus alignment and extract EC counts
Pre-computed BUS/EC files: Skip alignment, process existing BUS output
Pre-computed RDS: Load previously saved MPAQT counts directly