Process Short-Read FASTQ Files (Single-Cell)

This function is deprecated. Use mpaqt_prepare_short_reads_sc() instead.

mpaqt_process_short_reads_sc(
  fastq_1,
  fastq_2,
  index,
  clusters_file,
  output_dir,
  technology = "10xv3",
  threads = 1L
)

Arguments

fastq_1

Path to first FASTQ file (contains barcode + UMI)

fastq_2

Path to second FASTQ file (contains cDNA)

index

An mpaqt_index object

clusters_file

Path to cluster assignment file (barcode, cluster columns)

output_dir

Output directory for results

technology

Technology string: "10xv2", "10xv3", or "10xv4"

threads

Number of threads (default: 1)

Value

A list of mpaqt_counts_sr objects (invisibly)